hi there, i think i have resolved the issue, at least on my system (win7, t flight stick):
1) merged install (sf2, sf2v, sf2e, sf2i, exp1, exp2, sf2na), to get full march 2012 (no further patches) version;
2) key and joysick mapping at will (rename and backup your layout, just in case);
3) install mod (i tried with nf4, but it could work even with );
4) since the game at this point won't start (due to nf4 requiring latest patches, black screen on mission start), apply the full set (mar12hotfix, apr12, may12, jun12, jul12) of updates.
your key+stick mapping will be seen as the default one, but you won't be able to modify it due to updates deficiency (aug12 patch anyone?), so perform carefully step n°2.
since the last post is from june, i don't know if you ever solved the issue, if not, try this solution and good luck!
Will