I've been trying to play heroes of might and magic 3 recently but whenever I launch it my cursor shows the loading icon then it goes away and it says its running in task manager under processes. The program then takes almost an hour to open before finally working. I've tried using the HD mod and it does the same thing. I'm on 64 bit windows 7 if that helps.

Have you tried launching it again?
I have the problem with some Windows games that I need to double click the icon twice before it "takes".

Is rundll32.exe running after launching the game?
It can be old problem with Game Explorer. You need to disable it somehow:
https://www.gog.com/forum/general/games_explorer_gameuxdll_and_rundll32_issues_with_offline_gaming

I've tried relaunching it and rundll32 is not running, I changed the registry still just to make sure but it's still taking around an hour to launch :(