Hi,
There is a reason which I won't go into why the recently opened items are not available if you use multiple instances of TG2, but they aren't. It's related to the reason they don't show up after a crash. The recently opened items are read when TG2 starts and then written back out when it quits. If it crashes this doesn't happen so they aren't there to be read next time you start.
The reason for this behaviour is essentially robustness. I didn't feel the recently opened items were important enough to go to extra lengths to preserve them robustly in the case of a crash (which shouldn't be happening anyway), which might happen while a file is being loaded for example. I feel they're a convenience and not particularly important. However I see that other people feel differently so I will look into making them remain across crashes and multiple instances.
I've never experienced the recently opened items not being preserved across sessions when multiple instances aren't used and there hasn't been a crash. One situation you need to keep in mind is that if you move a file (should only be a problem on Windows) or have it on a removable drive which is not mounted when TG2 starts up then that file won't appear in the menu.
Regards,
Jo