First, what are your sound board settings? For Touhou generally you should use PC-9801-86.
Having said that, I suspect it's the way you're loading the PMD driver. I know that when I tried loading PMD.COM then ran MS the last two FM channels were missing. Try extracting PMD48O.COM and running the PMD86.COM instead, I suspect that will work (incidentally, what test files are you using? I need better ones).