The installer sets (or, more precisely, reset to default), some Compatibility flags that might have been set either by other addons, or by Windows itself, if FSX crashed for some reason. Some are hidden in the registry, so they are not immediately obvious.
That's why, you can be easily mislead thinking GSX "requires" a reinstall, only because something else has changed your FSX compatibility flags in the wrong way, and the installer simply put them back as they are supposed to be.
