Indeed, Windows 98 provides some features for troubleshooting IRQ issues. In my practice, such problems were not initially observed on the old AGP hardware, up to Conroe865PE\775i65GR3, but after the next upgrade to a system already equipped with PCI-e, I first encountered oddities related to IRQ operation and this was exactly repeated, regardless of the chipset manufacturer and BIOS version. So, in total, I tried 4 different motherboards, but the problem with IRQ was the same everywhere.
As for your specific case, obviously you are trying to do this from a normal WINDOWS session. Try changing the IRQ for the problem device in safe mode. And perform a reboot. It is worth noting that switching to manual management also implies manual configuration of other resources (Memory Range, Input/Output Range), and they also need to be configured correctly if you change the IRQ. As a rule, the correct values can be spied on in Windows XP and transferred from there (If everything works correctly there), with the exception of the IRQ itself, which under Windows 98 is selected individually for the problem device and usually does not coincide with what XP assigns, because there, as a rule, the PIC is not used at all and IRQs are assigned in a different way.
In my case, the problem was repeated with an Intel network card on different PCI-E hardware. It did not want to work with the default IRQ 5. Only primitive ODI and NDIS drivers worked. A full-fledged 32-bit driver refused to be confused. I didn't know about managing IRQ in safe mode yet, but I managed to localize the problem with another method of troubleshooting IRQ. Namely, reserving the IRQ that causes problems:
In this case, the system hides the IRQs specified in this field (in this case, 5) and the problem devices are redistributed to other free IRQs, even if they were not previously used. So my network Intel "moved" to IRQ6 and started working fully, as before, on an older AGP hardware. Reserving resources turned out to be a very useful tool for fixing hardware problems in Windows 9x.
What is noteworthy, manual installation at the DOS stage using tools such as Read Universal-for some reason does not lead to anything. If I change the IRQ under DOS, it will still change in Windows (unless reserved, as shown above, or manually set in safe mode, of course).