Sure man! Nestopia for the most part will play hacks, translations, with no problem but back around 1.37 i think it was basically changed that certain mappers were moved to the database.xml file exclusively for some reason and you needed to supply the pin wiring info, etc.
The mapper Ganbare Goemon Gaiden 2 is on is one of those mappers. The database.xml has a bunch of crc's attached to those games on those mappers. If you play the original unmodified game then it is fine, but when you apply the patch to the game it alters the crc and when you go to load the game it will throw the unsupported mapper error because the crc's do not match. The mapper is obviously supported, so basically after patching the rom, if you add an entry into the xml file for it with the correct info, when the game loads it will find the crc and work correctly.
This is the reason why ALOT of the konami famicom games especially throw that error. It's pretty silly. Easy to add, but silly nonetheless, at least to me.
Let me know if that makes sense.