We currently have a similar file size check in limitation using Microsoft SQL server 2005 and the SQL JDBC Driver version 2. The suggested alternative was to download and install SQL JDBC Driver version 3. However, that version fails to work on the JAZZ server, as documented in Enhancement 113697. Something to do with the JAZZ server expecting case sensitivity and Microsoft doesn't do that, but might when version 4 comes out someday. I'm sure there would be no issues if you are using DB2 for your database.

Another idea, if this is not a database error, we will get the "error uploading file" when checking in certain binary files. Our workaround, right click the file name in Package Explorer (or Project Explorer), refresh and try again.