Maybe the log below can help to solve it:
----------------------------
Session "default" started at 2015-08-20T17:40:05+0000
#1 DEBUG: SQL ERROR: Query failed with message 'MySQL server has gone away' - SELECT * FROM `fo_tab_panel_permissions` WHERE `tab_panel_id` = 'mails-panel' AND `permission_group_id` IN (45) LIMIT 0, 1
#2 FATAL: exception 'DBQueryError' with message 'Query failed with message 'MySQL server has gone away'' in /home/bc/www/sistemas/organiza/environment/library/database/adapters/AbstractDBAdapter.class.php:395
Stack trace:
#0 /home/bc/www/sistemas/organiza/environment/library/database/adapters/AbstractDBAdapter.class.php(313): AbstractDBAdapter->prepareAndExecute('SELECT * FROM `...', NULL)
#1 /home/bc/www/sistemas/organiza/environment/library/database/DB.class.php(213): AbstractDBAdapter->executeAll('SELECT * FROM `...', NULL)
#2 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(282): DB::executeAll('SELECT * FROM `...')
#3 /home/bc/www/sistemas/organiza/application/models/tab_panel_permissions/base/BaseTabPanelPermissions.class.php(104): DataManager->find(Array)
#4 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(338): BaseTabPanelPermissions->find(Array)
#5 /home/bc/www/sistemas/organiza/application/models/tab_panel_permissions/base/BaseTabPanelPermissions.class.php(134): DataManager->findOne(Array)
#6 /home/bc/www/sistemas/organiza/application/models/tab_panel_permissions/TabPanelPermissions.class.php(20): BaseTabPanelPermissions->findOne(Array)
#7 /home/bc/www/sistemas/organiza/application/functions.php(812): TabPanelPermissions->isModuleEnabled('mails-panel', '45')
#8 /home/bc/www/sistemas/organiza/application/layouts/website.php(297): module_enabled('mails')
#9 /home/bc/www/sistemas/organiza/environment/classes/template/Template.class.php(85): include('/home/bc/www/si...')
#10 /home/bc/www/sistemas/organiza/environment/classes/template/Template.class.php(73): Template->includeTemplate('/home/bc/www/si...')
#11 /home/bc/www/sistemas/organiza/environment/classes/template/template.php(47): Template->display('/home/bc/www/si...')
#12 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(148): tpl_display('/home/bc/www/si...')
#13 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(101): PageController->renderLayout('/home/bc/www/si...', '')
#14 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(63): PageController->render()
#15 /home/bc/www/sistemas/organiza/environment/classes/Env.class.php(159): PageController->execute('index')
#16 /home/bc/www/sistemas/organiza/init.php(178): Env::executeAction('access', 'index')
#17 /home/bc/www/sistemas/organiza/index.php(7): require('/home/bc/www/si...')
#18 {main}
#3 ERROR: Error: Cannot modify header information - headers already sent by (output started at /home/bc/www/sistemas/organiza/application/layouts/website.php:5) in '/home/bc/www/sistemas/organiza/environment/functions/general.php' on line 419 (error code: 2)
Time since start: 1.99475908279 seconds
-------------------------------------------------------------------------------
Session "default" started at 2015-08-20T17:40:52+0000
#1 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#2 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#3 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#4 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#5 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#6 ERROR: Error: mysql_fetch_array() expects parameter 1 to be resource, boolean given in '/home/bc/www/sistemas/organiza/application/functions.php' on line 1770 (error code: 2)
#7 DEBUG: SQL ERROR: Query failed with message 'MySQL server has gone away' - DESCRIBE fo_max_system_permissions
#8 FATAL: exception 'DBQueryError' with message 'Query failed with message 'MySQL server has gone away'' in /home/bc/www/sistemas/organiza/environment/library/database/adapters/AbstractDBAdapter.class.php:395
Stack trace:
#0 /home/bc/www/sistemas/organiza/environment/library/database/adapters/AbstractDBAdapter.class.php(313): AbstractDBAdapter->prepareAndExecute('DESCRIBE fo_max...', NULL)
#1 /home/bc/www/sistemas/organiza/environment/library/database/DB.class.php(213): AbstractDBAdapter->executeAll('DESCRIBE fo_max...', NULL)
#2 /home/bc/www/sistemas/organiza/application/models/max_system_permissions/MaxSystemPermission.class.php(15): DB::executeAll('DESCRIBE fo_max...')
#3 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(642): MaxSystemPermission->getColumnValue('permission_grou...')
#4 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(506): DataManager->cacheItem(Object(MaxSystemPermission))
#5 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(303): DataManager->loadFromRow(Array)
#6 /home/bc/www/sistemas/organiza/application/models/max_system_permissions/base/BaseMaxSystemPermissions.class.php(116): DataManager->find(Array)
#7 /home/bc/www/sistemas/organiza/environment/classes/dataaccess/DataManager.class.php(320): BaseMaxSystemPermissions->find(Array)
#8 /home/bc/www/sistemas/organiza/application/models/max_system_permissions/base/BaseMaxSystemPermissions.class.php(131): DataManager->findAll(NULL)
#9 /home/bc/www/sistemas/organiza/application/models/max_system_permissions/base/BaseMaxSystemPermissions.class.php(133): BaseMaxSystemPermissions->findAll(NULL)
#10 /home/bc/www/sistemas/organiza/application/models/max_system_permissions/MaxSystemPermissions.class.php(13): BaseMaxSystemPermissions->findAll()
#11 /home/bc/www/sistemas/organiza/application/layouts/website.php(362): MaxSystemPermissions->getAllMaxRolesPermissions()
#12 /home/bc/www/sistemas/organiza/environment/classes/template/Template.class.php(85): include('/home/bc/www/si...')
#13 /home/bc/www/sistemas/organiza/environment/classes/template/Template.class.php(73): Template->includeTemplate('/home/bc/www/si...')
#14 /home/bc/www/sistemas/organiza/environment/classes/template/template.php(47): Template->display('/home/bc/www/si...')
#15 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(148): tpl_display('/home/bc/www/si...')
#16 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(101): PageController->renderLayout('/home/bc/www/si...', '')
#17 /home/bc/www/sistemas/organiza/environment/classes/controller/PageController.class.php(63): PageController->render()
#18 /home/bc/www/sistemas/organiza/environment/classes/Env.class.php(159): PageController->execute('index')
#19 /home/bc/www/sistemas/organiza/init.php(178): Env::executeAction('access', 'index')
#20 /home/bc/www/sistemas/organiza/index.php(7): require('/home/bc/www/si...')
#21 {main}
#9 ERROR: Error: Cannot modify header information - headers already sent by (output started at /home/bc/www/sistemas/organiza/application/layouts/website.php:5) in '/home/bc/www/sistemas/organiza/environment/functions/general.php' on line 419 (error code: 2)
Time since start: 4.80886411667 seconds
----------------------------------------
Yes, it worked great, thanks! 
But, I still have an old problem. After login FO is showing just the logo line, including my user picture, below, everything is blank!
What to do now? I'm worried, because other users are trying to use the system, but without success! 
Thanks again.
Here is what I got from the development team:
Try commenting lines 414 to 416 in the file:
public/upgrade/scripts/ButiaUpgradeScript.class.php
The commented code should look like this:
/*
$upgrade_script .= "
ALTER TABLE `".$t_prefix."objects` ADD INDEX `type_trash_arch`(`object_type_id`, `trashed_on`, `archived_on`);
";
*/
After that, try running the upgrade again.
Does that work?