We recently upgraded from 2.0.4 to 2.2.1 and began experiencing intermitent issues with uploading files.
Occassionally when trying to upload a file we will receive a message that the file exceeds the upload limit. Our server is set to 20 MB file max and we are getting this erro regardless of the size of the initial file. I have been able to upload 15 MB files without issues and then seemingly randomly get the error when trying to upload a 100 KB pdf.
There also does not seemt o be a pattern. I can try the same file repeatedly and after the third or fourth attempt, the file will upload successfully.
I know this is not the most detailed post but I would love to hear if anyone has run into anything similar.
Since your server limit is ok, you have 3 more places to check:
1) Site Administration > Security > Site Policies > Maximum uploaded file size
2) Site Administration > Courses > Course default settings > Maximum upload size
3) In a course go to Settings > Maximum upload size
You'll probably find that one of those was set too low.