Changing time signature changes note pitch

v1.0 Windows 7 64bit

I have a downloaded midi in 6/8 which seemed fine in Musescore.
I then imported it to FLStudio (which seems to convert everything into 4/4) & exported it again with no changes. Opened the exported file in Musescore and changed the time signature back to 6/8. Expected problems due to bar line moves affecting ties/slurs and note length. Duly noticed some. Thought it was just an inevitable loss due to FLStudio, but then noticed that the pitch of a note appeared different. Not sure if it is that or just one note disappearing. I assume it can't just be a FL corrupted file because Musescore reads it fine and just produces this change when changing the time signature.

I also tried taking the original midi & then changing time signatures in Musescore 6/8>4/4>6/8, but found that the conversion just inserted rests in the 4/4 version which it happily removed again to go back to 6/8. I'm not sure adding rests is what I would really mean by a time signature change, but couldn't find a setting to change this behaviour.

I did try looking for the problem in the forums, but did not find an exact match. I can see it is a difficult thing for Musescore to do though.

I will try uploading the original FL exported midi file again (1st time it crashed in Opera - trying Chrome now - & I lost the content of my post). The problem is visible on the gt.1 stave, 2nd bar.