IIRC, the first time the FB01.DRV driver sends the patch banks there is an error, but subsequently (run the game again in the same session) there is no error. The two large sysex messages containing the patch banks are identical each time, and match Cloudschatze's dumps exactly, which implicates preceding messages.
There is indeed a difference in the preceding messages between the first and subsequent runs.
F0 43 75 00 00 01 00 F7
F0 20 F7
F0 00 F7
The 2-3 byte messages appear malformed and may simply be ignored. The first message of the first run is suspect because it does identify as a Yamaha FB-01 message, but I'm unable to determine its purpose from the data here.
To test the theory that this unknown message is causing the error, I've attached a .syx file that prepends the message to the known-good messages for the patch banks. If it turns out that the message is responsible for the error then perhaps there is a MPU-401 compatibility issue in the emulation that causes it. If it's not the message itself that's an issue then perhaps there is an element of timing, although I believe that delaysysex has been tried.