Jeff:
Have you been able to pinpoint the problem here? I am having the same problem since the upgrade to 1.0.1.1. I have been able to get around it by using DTaskManager which allows me to open all windows of a live process, but that is a bit of a nuisance. I have looked around on the net to find others having similar problems with any application, and the ones I find all are due to the program itself, so I can't fix it on my end. I am willing to help you track down the problem if you need me to.
In the meantime, if anyone else having this problem wants DTaskManager, go to http://dimio.altervista.org. It's freeware and has a bunch of nice features that go way beyond Windows Task Manager. It even allows you to trim RAM usage to make sure programs aren't hogging memory.
Regards,
Brian