Steps to reproduce (I recommend dialing the tempo down to ~20 bpm to make things easier to see):

1. Open LMMS and create an empty pattern on the tripleosc track.
2. Open said pattern in piano roll, hit play.
3. Hit pause in the piano roll.
4. In the song editor, move the playhead to some non-zero position.
5. Hit play in the song editor.

The Bar:Beat:Tick counter should reset and begin counting from 1:1:0 (or 0:0:000 if M:s:ms), however the playhead will not reset, and they will thus be in a disagreement over what time it is.

If notes are added to the pattern, you will hear them play according to where the playhead is, and not what the timer says.

A gif for your viewing pleasure: