Using 0.39a. Steps to reproduce:
1) right-click a directory of music files, choose "Play in foobar2000"
2) In fb2k, double-click a track after the first (i.e., 02, 03, etc.). fb2k starts playing that track.
3) Click "Stop"
4) Choose Playlist|Clear
5) Back to Windows Explorer, right-click same folder again, and choose "Play in foobar2000" again.
6) fb2k loads the directory but starts playing the same track as in step 2 above.