I see similar behavior using FreeScan and ProScan. On my BCD396XT, I permanently lockout several unlabeled TGs and half the time they won't transfer from radio to software. And the times it does, it doesn't put them back in the radio when I upload the file back. I noticed it only does that with unlabeled TGs. The permanently locked out TGs that are labeled seem to transfer back and forth just fine each time. Not sure if this is a software or scanner or user issue. 
Sorry if this has been discussed before, I tried searching but didn't find anything related.
Sorry if this has been discussed before, I tried searching but didn't find anything related.