Hi phlatt5th, yeah it has something to do with the system launchd process getting confused and messing things up. A whole lot of the OS depends on that but it's unfortunately kind of fragile and not all that robust like you'd kind of want a highly dependent piece of the system to be.
I think you may see some problems with the original v2.5 as well when you launch it a second time after recently quitting it, the first launch seems to go ok.
There is a new version of Wineskin that's almost ready to come out which looks like it fixes some of these specific issues so I think it should not be too much longer before I'll be able to make a version that should work properly on Mountain Lion.
I do have to say that it's kind of frustrating to experience this Apple rollercoaster of breaking changes already so soon...
- Michael
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