Hi Sciss,
fact of the matter is that the Aqua Tcl/Tk GUI on OSX interferes with audio processing in an entirely unacceptable way. When I want to do serious PD audio work, I boot Gentoo PPC Linux. Quite a bit of optimization for video/3d has been done for the OSX version of PD,. This was mostly for GEM, as PDP and PiDiP remain quite unoptimized. But audio doesn't seem to be a specialty/priority for the developers right now. I base this on comments from James Tittle and others when I brought this issue up before. I've also gotten feedback from others on this list that PD+Audio+OSX is on the border between crippled and useless in its current state.
One suggestion which HC Steiner made (IIRC) is to compile PD against a Fink or DarwinPorts X11 version of Tcl/Tk instead of the Aqua one. This entails some makefile buggery which I haven't gotten around to yet.
Another suggestion is to make sure that the realtime priority flag is disabled on OSX with the -nrt flag. This seems to be a workaround in some cases, but not a solution to the problem.
best, d.