Dear Bill,
Actually this is not what we could qualifiy as a tool bug but instead an SDK bug. The tool is reading a property that should reply 0 and that replies 1.
This has been fixed in latest rollup packs for 4.0.
The only workaround for now is to replace entries in the export files, they'll be imported as written in the file.
Regarding App Manager, I've checked and was not able to reproduce, all was fine on my 4.5 HRP 03 / HR 04 dev environments.
Best Regards,
Pierre