Recently I made a bonehead mistake and created a merged patch while keeping both FO3edit and FOMM open - definite no, no. This has had the effect of:
1 FOMM not closing when FO3 is started.
2. FO3 crashes when the wanderer enters almost any new area ( most notably, Megaton.)

I'm thinking that my mistake has screwed up FOMM (for FO3, also have NV installed but it is unaffected and both NV and FOMM continue to play nice together.)
Anyone have a clue as to how I can fix this mess? :banghead:

I think this might have occured because you changed out the merged patch you already had. Having these programs open would have had no effect on the output of the file whatsoever. Try removing the merged patch, making a clean save, then reenabling the merged patch and loading the game again.