I would assume you know how to set compatibility mode, but if you don't, right-click the Final Fantasy VII executable and go to the "Details" tab (not sure what it is called, it is the second tab, though) and check the compatibility mode box. I set it for Windows 98 mode and the speed of my game at the slow parts finally caught up with the normal speed.
For instance, my game would run really slow and glitchy on the world map (and crash inconveniently oftenly) prior to setting the compatibility mode, but after I did, it runs perfect. Maybe this would solve your problem?