Attached?
Educated guess ...
If site was upgraded from 2.9 to 3.3, there's a good chance php was also upgraded to a higher version. That might have reset php.ini to something lower.
Login as admin level. Go to Site Admin Menu, Server, PHP Info.
Version of php is shown there as well as the variables that control max uploads.
post_max_size and upload_max_filesize
IF below what you expected to see, contact server administrator.
In a course, check course settings for 'Files and Uploads' ... does the drop down list show site upload limit as the first option?
'spirit of sharing', Ken