I've read through this thread and feel for you guys with the problem (having been through similar in the past).
Putting on the analyst hat as an outsider it appears that:
1/ there are W7 builds that work and those that don't
2/ there are hardware configs that work and those that don't
3/ there are hardware configs that don't work with W7 but do with an alternative version of Windows
To me this indicates that the relationship between W7 and the hardware config is the issue.
In addition, the number of keystrokes (48) to reset the transport seems to indicate 2 keystrokes per remote layer channel are switching the USB controls into functional mode.
To go into solutioning mode it appears that W7 applies some USB settings within certain h/w configs that need to be unswitched (if they can).
Have the BIOS switch settings been compared between a system that works and one that doesn't?