If you want to do a rerip, then please use the
Neko Project 21 VGM mod.
S98 logs are often done with 100 or 1000 Hz. VGM logs are 44100 Hz, so the timing information is more accurate than when using an S98 conversion.
Aside from that, I assume that the S98 logs didn't record the "6ch enable" register state. (register 029h, value 80h)
The YM2608 defaults to YM2203 mode and it needs that command in order to enable YM2608 mode.
You can test this by hex-editing the VGM file. At offset 00E0h, overwrite the first command (56 30 xx) with 56 29 80 (YM2608 mode) or 56 29 00 (YM2203 mode).
I think S98 logs often don't have that command and the player automatically enforces YM2608 mode by itself.