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Gotcha -- thanks for your quick response! I've since tried some things successfully, and I'll write the following in case any other interested Mac OS X people might be helped by it:

I first figured out that I was using an older version than I thought I was...

Tried to compile the latest version for Mac OS and quickly gave up (seeing as I'm a complete non-programmer with zero experience/knowledge in this department, and I wasn't able to locate/install the exact qt library version it seemed to want ... a later one didn't work).

The newest ready-made .dmg build of qjackctl that I could find was 0.3.6, and there's a link to it (in 64/32-bit and 32-bit versions) here: http://sourceforge.net/p/floctrl/wiki/configuration/

I installed the version for intel 32/64 machines, and updated my Jack OS X version to the corresponding one (for some reason, I only had the 32-bit version before).

The MIDI-related issue is unchanged (which is alright; I can route my MIDI through Max/MSP, anyway -- but I will see if your jack midi driver setup suggestion helps, thank you!) But on the positive side: I risked trying the system tray option, and it works reasonably well. With one "unexpected" behavior: when in the system tray, qjackctl (whether server is actually running or not) will _always_ interrupt computer shutdown and demand attention. If one cancels shutdown, qjackctl closes automatically and one can then successfully shut down the computer with no interruption. There is of course no interruption to shutdown if you quit qjackctl beforehand.

So for me, it's still seems to be a good option: whenever I'm frequently doing music with this machine, I can put qjackctl in my startup items with the "start server at startup" option checked. The patchbay's storage of the connections I need works perfectly. These two things mean that, for me, it seems to be a better option than Jack Pilot, because I spend a lot less time loading and setting up things.

Thanks once again for replying!