On Windows 7 64bit there is a issue with Application.Quit(). The app does not quit and freeze instead. Any thread is joined() and there’s no problem with Mac and Win32 bit version.
I can not replicate your issue - I have built 64-bit exes in probably every beta and release candidate version of 3.5 and have never seen what you describe. It sounds like there’s something more going on here - you’re doing thread operations, and perhaps other things that are breaking the quit operation. My suggestion would be to create a simple project (with just a camera and script that quits), verify that that works, and then start slowly adding elements from your current project until it breaks.
BTW: did you have a question you wanted to ask, or are you just reporting a bug? If the latter, I suggest submitting a bug report directly to Unity.