You're hitting two separate issues here. One is a compatibility issue, the other is simply a matter of configuration.

The issue with the Sound Blaster Live and Audigy is the infamous "Via SBLIve PCI bug". Actually that's not a strictly accurate name. Creative's engineers used a number of features in Intel's PCI implementation that were not strictly in the PCI spec. Via only implemented the spec. Result was that the cards had big issues. Generally the advice was avoid the combination of Via 686A/B southbridges and Creative SBLive/Audigy cards (it wasn't exclusively a problem with SBLive, it also occurred on some TV cards). That said it wasn't impossible to get them to work on Via chipsets, just a pain. Bottom line was that interrupt line sharing failed to work. Interrupt lines aren't the same as IRQs, there are 4 interrupts on a PCI bus like this. Each slot is connected to one of them, as are the integrated PCI devices (i.e. IDE, USB and audio) and the AGP slot. If you're lucky one PCI slot won't be shared with any of that. If so and you can find it (by trial and error), the SBLive/Audigy should work decently. If...
(note that if you hit the same interrupt as the IDE, massive data corruption might ensue 😦 )

As for the ES1688, that's simple: it's a non-PnP chip so there's nothing to detect. You need to configure resources (either with jumpers or with a (DOS) config tool) then tell Windows 98 what they are by telling it to manually search for device, selecting the ES1688 (or failing that just Creative SBPro2) from the list and entering the resources you configured.

Can't comment on the CX4235-XQ3, as that supports PnP so should at least get detected. Maybe legacy ISA PnP is disabled in BIOS?

But...

The MS-6309 has integrated sound with a game port on it. If you just need the game port, that should do the trick. It also does decent SBPro2 in DOS, and AC'97 in Windows, which is good enough for anything non-positional. Why not just use that?

Any chance the ISA slot is bad? You have anything none sound card, like an ISA VGA card you could test?

One thing to watch for in general with the MS-6309 is bad caps; MSI was one of the worst-hit vendors and this was one of their worst-hit boards. I had to support systems with these boards in them and the flood of RMA started in late 2000 already. Bad caps can have all kinds of effects, which might include buses not functioning. Or maybe not - but check those caps regardless unless you've already done it thoroughly.

As for integrated it also isn't detected at all. But there is one capasitor that started leaking and one that will start to leak soon, so maybe that's the problem

ksiumaxx wrote on 2022-06-20, 20:07:

As for integrated it also isn't detected at all. But there is one capasitor that started leaking and one that will start to leak soon, so maybe that's the problem

If any one cap of a given type is leaking or bulging, replace all caps of the same type *immediately* before using any more. Usually your board just deteriorates into complete instability, but sometimes the caps can cause parts to get voltages or currents they weren't designed for. We had one case in early 2001 of one of these boards where a MOSFET had somehow shorted after the caps near it failed (my best guess: leaking electrolyte did the trick). It literally melted/burnt a hole straight through the PCB.

That said, I suspect there might be more going on if you have identical trouble with devices on ISA, PCI and AC'97 - that sounds far more like messed-up BIOS. After fixing the caps, I'd recommend a BIOS flash with latest version and then reset to factory defaults.