During installation, ubuntu checks all discs for errors and FINDS errors on VFAT drives that are actually clean.
During installation, Ubuntu correctly asks if the errors should be fixed and, of course, you say no.
Ubuntu then installs and reboots. On reboot, Ubuntu scans all drives using dosfsck set to automatically "fix" errors. The "errors" were all "illegal file name" and were all files/directories with (legal on VFAT) spaces in the name such as "C:\Program Files",
Ubuntu only declared SOME files with spaces illegal, not All.
THIS IS A CRITICAL BUG AS IT CAUSES ubuntu TO ERRONEOUSLY MODIFY ALTERNATIVE OPERATING SYSTEM FILES.
In the short term:
If you MUST scan other operating system discs before mounting them, you should give users the option to "NOT FIX and Don't Mount" / "Not Fix and Mount anyway" / "Fix and risk the consequences"
Or perhaps just don't mount any disk ubuntu THINKS has errors.
In the long term you should fix dosfsck so that it doesn't pick up false errors on VFAT drives.