Seems like Ducati is using the 30 or 40A (large) fuse as a "main fuse" in the last few schematics that I looked at. (This was on a 1098, 1198, and 848--I was looking at the U.Manuals that you download on-line for info on the alternator sizes.)
Anyway, DUC used to use the big fuse as just a Reg.Rectifier fuse, but as I mentioned, it looks like they use this fuse as a main, now. Also, it appears that on these SBK machines, that this fuse is now placed right on the starter solenoid.
Maybe the "new" Monsters are like that. That's where I would start looking. Shouldn't be too far from the battery.
Try this home-cure-all: Shove a DUC between your legs.
Present DUC: 2003 ST4S Yellow! 2001 ST2 Blue
Past DUCs: 1998 ST2, 1981 500SL Pantah, 1985 MHR Mille, 1987 Paso Limited, 1995 916 mono
Other brands (past):
1978 BMW R100RS Motosport, 1978 R100S, 1981 Moto Guzzi V50 Monza, and a long list of Hondasakizukis