I tried to replicate the issue with your files, but failed. There were some variables that I couldn't quite emulate though, so still some uncertainty as to whether or not I did fully replicate your setup.
Perhaps next time you do interlinear in PT, you could video your screen, showing one instance where interlinear creates the extra sense in FLEx? Then at least we could see the exact steps you are using.
Or let us know, and we could join you online to watch / help you investigate?