@Great Hierophant helped me today telling me how to check if the MPU401 is responding at all. So, maybe you can do as 1st test the following:

1C:\>debug --> that's DOS DEBUG.exe tool
2-o 331 ac
3-i 330
4FE --> Command Acknowledgement response 
5-i 330
615 --> MPU Version 1.5
7
8-o 331 ad
9-i 330
10FE --> Command Acknowledgement response 
11-i 330
1201 -->  MPU Revision A, i.e. Version is 1.5A
13- q

so, that's the only advice I can give you... I don't know if it's helpful in your case, it was helpful in my case to realize the MPU-401 communication is broken.

Jackhead wrote on 2023-10-12, 19:42:

[...]
So i have a MPU-401AT with a midi board installed and it put out midi and same time audio over RCA if a midi modul is installed on the header.
Did the LAPC work different? pretty sure its same on pc as on pc-98. So maybe some LAPC user here can help?

I know nothing about PC-98 systems but I do have a LAPC-I. With it you just tell a game to use MPU-401 and you just get sound from the audio jacks.
LAPC-I is also one of the ISA sound cards that need -5v to work fully: lack of this will result in a silent card so maybe this is a hint for your PC-98 system? -5v rail is OK and available?

I have a PC-98(21N), but not the LAPC card, instead the C-bus Roland MPU module, and that just works as any normal MPU interface would, though that's not helpful to you

Is your card perhaps jumpered to disable the onboard synth and instead only pass through to the MPU header?