If data doesn't make it over to the new pilot file during the conversion, that's not corruption. That's just a broken pilot converter. That converter hasn't been tested as much as other parts of the pilot code, so I'm not surprised it's not working flawlessly yet.
Just to clarify, when you run an Ant8 build, it converts your old player files to a new file, not modifying the original file (or it should not anyway). That's why using a non-Ant8 build should still work fine, and not have noticed any changes made by the Ant8 builds.
If after the conversion, whatever made it over still has other problems after using just an Antipodes 8 build, like things still won't save, or settings disappear, or the game crashes because of the new pilot file, then yeah, that's probably corruption.