Yep, it's a definitive bug. '-R' does not handle very well the special case
when realtime capabilities are not allowed.
I'm not certain, of the top of my head, what this is, which version of MusE is
it? I run MusE 0.6.3 always with -R. Is jack perhaps not started with -R ?
(it's pretty much a requirement there too)
-R instructs MusE to set certain threads to realtime-scheduling (SCHED_FIFO)
to improve performance. This applies to the audio-thread and the midi-thread.
When you are running through Jack the audio-thread is implicitly set to
SCHED_FIFO thus removing the need. I'm not sure, however, if the same applies
to the midi-thread. In MusE-cvs '-R' is removed (since MusE now requires
Jack) so, there the question is moot.
In any case, if you are running with jack at a fairly small buffersize (<512)
the jitter will probably not be very noticable even if it's there. To make
sure there are no problems lurking about, run jack with 2048 buffers and play
something monotone, e.g. a hihat line.