So if an Opus window was open before AD was started, AD hangs when it opens a file?
This seems really strange since, as you noted, just closing Opus's windows does not actually exit Opus (unless it's configured to, which isn't the default). I guess it may change what the hooks do but the hooks would still be there.
(Info on the hooks can be found here, in case it helps guess where the problem is happening. There's also a desktop double-click hook, if you have that feature enabled. All hooks are installed using the standard Windows API.)
Do the crash logs indicate which message is being processed when the crash happens? Is it consistently the same message?
Do the crash logs indicate which module (DLL or EXE) the crash occurs in, or give a stack trace?