Interesting thread.
Some additional observations:
1. Myself and Tarekith have both observed agravation of arpegiator timing issues with a Virus TI (in old TI OS versions) when using an MD as the master clock.
2. I have observed issues which my V-synth when using it as a master clock - v-synth seems to have a bug which can sometimes make it incredably sensitive to clock jitter with certain fx in use - as evidenced by odd squeaks at times.
3. Using MD as master clock, push some of the trigger buttons. To make this extreme, simply run you finger quickly along the trigger buttons - this will causee a massive and very audiable slow down of the MD tempo and all clock slaved devices.
MIDI itself is a very hit an miss mechanism for syncing synths - you are allways going to get jitters due to other traffic on the cable that will be upto the length of the otehr message that is contending for the clock message. Typically this works out around 1ms or so, or 0.1 ms with the MD in turbo mode. I have regular observed far higher level for jitter from the MD, especally around pushing buttons on it.
Also I have tried to use it from live in pattern gate mode - this can only be made to work reliably by advancing the gate tracks. Obvious thought - just means that live is not properly syncing notes with clock, or midi interface lag etc. MIDI interface lag is ruled out by clock and notes going along same data path. Live is not ruled out, but I dont consider it a highly likely culprit as 8 otehr synths mange to trigger arps and switch arp note patterns perfectly well under identical circumstances.
The MD is a wonderful bit of kit, but it isnt perfect, its clocks are flawed relative to most other gear I have, but none the less for convenience I still use it as my master clock and live with its flaws. These flaws are a contributing factor is my regular thoughts about ditching the MD completely and buying an MPC2500 instead... I know different machines different style of use etc, but it would probably do the job and Im sure I would adapt
DAW/computers are not perfect, but most sample clocks are very good references on a decent quality audio i/o card - if they werent, all of our recording would sound like shit for reasons other than dubious musical skills
Also some DAW can be worse than others - Cubase 4.0, 4.01 have been particular bad, I havnt tried tests on midi in 4.02 and 4.03 yet. Live 6.0.3 isnt perfect either.