Well we have a resolution to the problem.
We found that the packages are stored in the SQL database table. When we enabled the 'finest' logging on the console we saw the following error.
"Could not allocate space for object 'dbo.BINARY_FILE' in database 'sem5' because the 'FG_CONTENT' filegroup is full. Create disk space by deleting unneeded files, dropping objects in the filegroup, adding additional files to the filegroup, or setting autogrowth on for existing files in the filegroup."
So we reduced the number of Packages and bingo we where able to upload the new version.
Maybe a takeway for Symantec here, the error messaging could be a little more informative.