Cruise, have you patched your .exe for 4gb? I've been having the same problem as you and ran across an old post regarding sh3.exe. In it's default (up to 1.4) state, it is only able to access 2gb of memory. You can patch it so it uses 4gb using this tool:
http://www.gamefront.com/files/21775767/4gb_patch_7z
I just did this and now I can actually load a mission with MFM.