Sorry to respond so late on this one (I have so many forums I’m a member of that I tend to forget to check a couple of them now and then).
Yes, the problem with playing MIDI while using JavaSound for sound effects, is that JavaSound handles both MIDI synthesis and audio mixing on the same thread (rather poorly), so while it is busy doing stuff with the MidiDevices, the Clips and SourceDataLines get ignored for a millisecond or so - enough to create undesirable “artifacts” (i.e. clicks and stutters). Unfortunately, this is a bug with the JavaSound API itself, so the only way around it would be for me to write my own MIDI synthesizer instead of using the JavaSound one (something I may do in the distant future, if I can get the rest of the library to a “final release” point). In the mean time, you already found the best solution: using OpenAL for the sound effects leaves JavaSound free to focus its full attention on MIDI synthesis.