For PAS[16] SFX, try using an 8-bit DMA channel like 3 as some games don't seem to work with 16-bit DMA. That's true at least for SC2000, I don't have the other games.

You probably don't have MVSOUND.SYS loaded. Sim City 2000, Warlords 2 and Transport Tycoon require it for its digital sound drivers to function.

Sim City 2000 uses AIL/32 sound library. Its PAS digital driver fails to detect the device if there is no MVSOUND.SYS loaded:

1                ELSEIFDEF PAS
2
3                mov eax,0bc00h            ; PAS, look for MVSOUND.SYS driver
4                mov ebx,03f3fh
5                invoke INT2F,eax,ebx      ; call DOS MPX interrupt through DPMI
6                xor ebx,ecx
7                xor ebx,edx
8                cmp bx,'MV'               ; MediaVision flag
9                mov eax,0
10                jne __exit                  ; No MVSOUND.SYS = device detection procedure reports failure
11                mov eax,1
12                jmp __exit

Warlords 2 and Transport Tycoon use DIGPAK sound drivers which also require MVSOUND.SYS:

Thanks for the hints!
Moving the DMA from DMA5 (16bit) to DMA3 (8bit) solved the problem with SFX, but the Output now should stack at 8bit quality?
Maybe someone can explain why 16bit DMA dont work with SFX but with music?

Regular i load the MVSOUND.SYS in the CONFIG.SYS in any boot configuration. I use the version, which is available in the PAS16 driver pack from VOGONS-Drivers

Command-line in CONFIG.SYS:
DEVICE=C:\PATH\MVSOUND.SYS D:3 Q:15 /S:1,220,1,5 /M:0,330,7 J:1 V:65

Yes, though in practice it doesn't matter as most DOS games only use 8-bit samples and 8-bit output anyway. There is a list of DOS games with 16-bit sound here: A List of DOS Games with 16-Bit Sound. Descent II, for instance, has separate 8-bit and 16-bit SFX tests in its setup program, using an 8-bit DMA leads to distorted audio in the 16-bit SFX test but 16-bit DMA works fine for both.
I suspect some older games were written for the original PAS and simply claimed PAS16 compatibility without having added support for 16-bit DMA.
FM synthesis (music) only uses port I/O, it doesn't use IRQ or DMA.
@bristlehog MVSOUND.SYS must be loaded for PAS cards to work at all, even as an AdLib for OPL2 FM.

Not sure if this of any help, but I would start REMing out EMM386 in config.sys (for testing purposes, at least).
On one of my 586 PCs, this solved all my issues with the PAS16.

jtchip wrote on 2020-01-05, 22:47:

Descent II, for instance, has separate 8-bit and 16-bit SFX tests in its setup program, using an 8-bit DMA leads to distorted audio in the 16-bit SFX test but 16-bit DMA works fine for both.

Funny, Descent was the game that came to mind when I thought of 16-Bit PCM / PAS16.

jtchip wrote on 2020-01-05, 22:47:

FM synthesis (music) only uses port I/O, it doesn't use IRQ or DMA.

Yup, but there's a catch.. 388h is not only used for OPL3, but also the control port of the PAS16. 😉

For SC2000, it's definitely a limitation in the game. I did try with and without EMM386, and it made no difference. Only changing DMA channel from 5 to 3 worked. This is on a 440BX-based system, having just taken my PAS16 out of storage.
I believe the original Descent only uses 8-bit audio (it's not in the 16-bit audio list) but at least it does work with PAS16 on a 16-bit DMA channel.

jtchip wrote on 2020-01-06, 00:37:

This is on a 440BX-based system, having just taken my PAS16 out of storage.

Ah, I see. Well, the PAS16 was made in ~92, before PCI, ATX and complex chipsets became comon.
Anyway, performing a diagnosis from the far is difficult, so I can only guess. 😅
Maybe some of newer standards are using some of the resources that used to be free on pure ISA systems (386/486).
For example: Bus-master IDE via PCI. Secondary IDE. Or ACPI/APIC (IRQ2/9). Disabling/switching them and other things to "Legacy/ISA-only" may solve some issues.
In AMI/Award BIOSes found on Pentium I systems (586), there's often an option for that.

Anyway, good luck! 😀

Edit: I forgot. PAS16 needs -5v, too. Please make sure your ATX PSU has it.
Edit: Some small editing done.