I'm actually not that worried about it for the most part. If it really got to me, I'd just patch the window style out myself since it wouldn't take but a few minutes at most. I just felt it was better to post things on here rather than fixing them for myself silently since not everyone has that luxury.
The refresh key was just an example though and even with that, it's used to pull up my web debugging tools in Firefox. I haven't taken the time to go through all the hotkeys affected. These are all the result of Windows finding the WS_POPUP style on that window without having a parent window set on it so it's just Windows doing what it does and we'd have to go through the list of default ones to know which of them all are affected. Setting the parent to the original window doesn't really change much except fix that particular problem so that it could only interrupt input to the program and not the entire desktop interface.
I'd be interesting in hearing about some of the other's though so I know which are known already in case I run across them if you have a few minutes to type up some of the one's you're aware of down.