I agree especially with the comment by the OP that it takes a while for the lock-up to happen. A drive issue related to garbage collection/memory leak could be the cause. And since it has been happening for a while and with previous versions of LR for the OP that is where I would start searching were I the OP. Or just rolling back to either an earlier brand specific driver for the mouse might help.
Also, as I mentioned, I use a vertical market app I use that ran into issues if the system tray icon was left enabled. Once you turned off showing the icon in the system tray, the whole prob disappeared. The head developer and I worked on that one for a while and it was only via elimination that we decided it was something in the MS code that polled the system tray icon and not related to the video sub-system. BTW, eventually that issue was resolved by some Win update, we never did figure out when, where or why...at which point we stopped caring!! hehehehe...
I don't remember is anyone suggested to the OP that one test might be to use the Windows generic mouse/trackpad driver to see if the issue goes away. Also, the OP might try uninstalling the associated software and just leaving the brand specific driver to see what happens.
Man, it's times like this when I do not miss the consulting game...of course it pays well...hehehehe...HEY....
Could the OP install MS Virtual PC then setup a clean Win7 x64 install in that virtual machine to see if the issue persists with just Win7 x64 and LR3 installed? That would at least confirm it is something between the OS and LR...if that runs OK, just keep installing other apps until it breaks in the virtual environment. I mean as a last resort sort of thing. MSVPC is free now and you can even setup an XP virtual machine to go with a true XP Mode while you are at it...then the OP would have an XP Virtual mode setup and also create the clean Win7 VM (making a copy of course so to create a new one all that needs done is to kill the broken one...
)
EDIT:
here is the link to a turnkey install of Win VPC and XP Mode under Win7 x64:
http://www.microsoft.com/windows/virtual-pc/download.aspx
it is really a no brainer setup...of course to run the XP mode it took me a good three hours because I went ahead and let the virtual XP machine install ALL it's updates...yeah, I was really bored...hehehehe...