I just noticed this recently, as I hadn't connected my vg8235 for a while, but my nms8250's fmpac sound is slightly different from the vg8235.
I also tried an emulator (BlueMSX) and it sounds like the 8235, not the 8250.
After some more testing I think that what I hear is one channel being slightly less amplified on the 8250.
I was wondering if this could be fixed; AFAIK this 8250 already has an fmpac fix though, as it was explicitly stated so when I bought it.

change resistors R428 and R429 for condensators 10o microF (max 25 volt).

then if it not the right balance between FM-pac and PSG you can mount a variable resistor (10 K) in line 49 of the cartridge-slot connectors. Then you can change the balance what you like

Why not add this to the FAQ, since it obviously is a FA one...

/me still remembers sending his NMS-8250 to Philips twice, after buiyng Nemesis2.
In the end, I went to Philips in Eindhoven with a Toshiba HX10 and my NMS8250 showing it to the people over there. (You could here it quite clearly when you started to play and the shuttle left the bay).
After that, they studied some books and drawings and indeed put a "potmeter" on line 49 and TFH was a happy camper.
Took me about 2 months in total, but it got solved

I have a "volume control" on an SCC itself, but not in the computer. So, the SCC sounds correct, the fmpac not, but I didnt spot it before as
A) Hadnt used the vg8235 for a while
B) In the old days I didn't have an fmpac; SCC or PSG differences I'd spot much sooner.

Also hear something off in the 8250's PSG... I did ask about that one before, but my technical skills are minimal and so is the diffference, so for now I left that. Placing a "potmeter" should be possible even for me though.

Really..the 8250...gotta love the desktop model itself, but the sound issues...bleh.

I had to change also the resistors in my SVI-738. Before you couldn't hear any FM/SCC, just the ultra-loud PSG.

Got a 8250 with a pana fm pac... this fm pac has a custom made sound output, so it doesn't have to go through the 8250... i'm quite happy with that...

*slaps head*

Doh! And I have something like that even! I normally use my panasoft fm-pac, but I also have a fm-stereo-pak with separate output. Thx for the idea; I feel somewhat silly for not thinking of it myself

It's good to *not* run your music through your computer...

trying this out revealed it; what I'm hearing is indeed the same as the SCC issue; it's not an fmpac channel being surpressed but (yet again, and understandable) the PSG. The issue happens when a song uses a combination of PSG and FMPAC.
I should listen better too as I feel I should've been able to tell a PSG apart from an FMPAC :S
The separate audio output kind of fixes it; I can adjust the tv volume to match up with the separate speakers for the fm-pac (as the internal MSX fmpac output is disabled if the other output is used; meaning you only hear the psg through the tv and not the fmpac), allthough it's a little strange that way. Either a "potmeter" or some nifty tricks with separate audio output (perhaps the latter could achieve much more amazing results) would do the trick.