generally there are different ones for euro and usa. 98, 99 are the same. 00 and 02 are the same. the softway lists the 01 as having the same ecu as the 750, which is obviously a mistake.
the 02 mapping is different tho i'm sure from the 01, which i think is different to the 00.
the 98/99 does not interchange with the later ones due to the side stand switch input the 00 on ones have. it may run, probably badly but most likely not at all.
is the reflashed one you have for your model? has the idle mixture been set properly?