The GOTY version contains expansions only (Knights of the nine & Shivering Isles). It doesn't has the plug-ins (Fighter's Stronghold, Horse armor pack, etc) you have to pay to get if that's what you meant.

As for the crashing - deactivate new plug-ins to isolate the one that caused the crash. From my experience some plug-ins do cause CTD. Which other mods you're using?