I just updated and the issue's still there:
I have a folder with track A, B and C.
I play track A and find it boring.
I skip to track B.
While listening to track B I delete track A from the folder (not just the playlist).
After listening to track B for X seconds i press stop (not pause).
When I press play again I will hear track C starting X seconds into the track, instead of expected track B.
If I delete two tracks the unexpected skip will also be two tracks forward.
I know I'm supposed to file a bug report att flyspray, but it might be nice for others to see the topic here also...