We have tested multitrack timing coherence on many systems as part of the Music Tech degree work, it's an assignment for the students to test phase coherence in stereo and multiple file inputs.
ProTools and Logic come out even with phase locked audio, there is no measurable movement in stereo or multiple sources, although USB hardware does have some issues.
Cubase wanders a little occasionally, and seems to be a function of how much work the DSP has to do on the input and what kind of processing power is avaliable.
Incedentally, output from multiple tracks is almost never a problem, outputting sine waves from a 2/6 into a 5.1 rig yields cycle accuracy, as does ProTools hardware from the 001 up.
I agree that the M-box mic amps suffer from a lack of power, but who wants to use the baby Focusrites anyway, they suck, you'd be much better off with a good stereo pre-amp and come in line-level.
The 001 is not a particularly musical interface, and the TDM 888 isn't a market leader by any means, but the new 196 interface on the HD range is very nice in both the digital and analog version, as is the 8 way mic pre, although I'm a big fan of Rupert Neve's work for Amek.
Sure the HD rigs are expensive, but they effectively replace an entire recording studio if need be, there is no longer the need to use a large format desk for recording, as long as the input stage and the monitoring are up to scratch, you can record/mix from the rig itself.
None of this helps the original poster, except to say that ProTools is still a force to be reckoned with in audio and post pro, but in the end you pays your money and you takes your choice.
I have an M-box LE system on my PowerBook for editing and remote tracking, and use HD1 or HD3 for heavier recording needs and mixing to stereo or surround formats.
I'm an enginner from the old school who genuinly venerates Neve, Harrison, Studer and 3M etc, but I really like the flexibility and functionality of ProTools.
If I was more MIDI orientated, I'd use Logic, which I think is probably the most complete production package. ProTools MIDI imp is not as good, but is still very usable.
Logic currently has problems on the G5, but they are under consideration, as is the 001 problem.
I'd recomend the Big Box Logic package, and live with the steep learning curve.