Serious audio glitch problem in 9.1.1 - please help!

Got a problem with audio glitching that is driving me insane - hopefully someone can help (please! :_))
I'm on Logic 9.1.1 on a recent MacPro using 10.5.8, 12Gb memory. I've created an arrangement in Logic with two multi timbral / multi-output instruments (Kontakt and Stylus RMX - both up to date versions) with aux outputs for all of the instruments channels; 16 in the case of Kontakt, 8 in the case of RMX.
I'll work with this setup and after a while I find that whenever I play and then press stop, a tiny portion of audio will repeat rapidly, over and over again in the 'master' left output channel at +6.0dB - it also shows up on all the instrument auxes at a much lower level. It's as if Aphex Twin has invaded my Mac... Weirdly, this problem crops up even if I'm not outputting anything from the multi-instruments - it's enough that say, an EXS instrument, plays something, I'll press stop, and then the glitch signal will appear in all the level meters of the multi instruments and master output, but not on the EXS level meter. If I press play again, the glitch disappears and audio playback is perfect - it only happens when stop is pressed. And no sign of it if there's a silent part in the arrangement with no tracks playing anything.
If I have any instances of reverb on bus channels, that audio will will also feed into the left channel of those busses, even when there are no channel strips sending to them. Weird as ****, and driving me up the wall with frustration.
I've omitted it being down to my audio interface (Metric Halo 2882) as the problem persists if I switch to the Mac internal I/O.
I'm trying to work through this at the mo as I've got a deadline for 2pm this afternoon - but I'm worried I might not make it due to throwing my feckin computer out the window. Please help - thanks!

Alasdair Reid wrote:
It's as if Aphex Twin has invaded my Mac...
If your deadline wasn't looming, I'd say buss everything to a stereo track and record this stuff. It sounds great, you could use it in another project later...
But to your problem: The only quick solution I can think of for you to try is to create a brand new fresh project and use the selective track import feature to bring your tracks into the new project. Don't start from an old template (that you may still be using since Logic 8 or something) because this could indeed be the root of the problem. Build a new template from Logic 9.1.1, then make a new project from that and import all your tracks. If it's your project that's corrupted somehow, this could be the trick to solve it, and it won't take too long to try, so it's worth a shot.
I'm not sure of this, but something is telling me I've seen this problem before, and if so it was on Leopard (not Snow Leopard) on a MacPro in the studio. Have never had it on my personal MBP (which was only ever Tiger and then Snow Leopard - I skipped Leopard on purpose because the studio machines seemed so very dicey). Also, I don't use RMX on my own machine but in the studio, yes. Same deal for multiple output instruments, I rarely do that either. On that point, another thing you could try is to forget about multiple outs for now, and just work with stereo instances. Yes I realize this will mess up your entire painstakingly built-up mix.. but if this is causing the flakiness you may have no choice but to go back to stereo instances, finish your writing, then do the whole mute/solo thing to bounce your individual parts to audio and proceed from there. In this scenario, selective track import will be a timesaver too because once you've done all the bouncing, you can just create a new project and import all of your channel strips and so on, to then re-assign the individually bounced tracks to the assignments you had before. Will be quicker to recreate your mix than having to do it from scratch. Or you might not even need to do this step because if eliminating the multi-out instruments makes the prob go away, then you can just recreate your assignments within the same project using the bounced audio tracks.
Get to it.
Once you've delivered.. I'd open that project again and record all of that lovely Aphex Twin messiness for later use.

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