About the upload directory, whenever you delete an email/file from the trash, it should also get deleted from the upload folder.
Remember that every single email is stored there as well..
I doubt this is the problem as otherwise you would not be able to do tons of things but.. have you checked the permissions?
Regarding the objects linking list, we have yet to fix some stuff there (for a future version), but this issue you mention should not be happening..
Best regards,
Francisco