I have switched back to GA-5AX. The main reason for that was a mysterious issue with audio in Windows on the Shuttle motherboard: Garbled sound in Windows 98
I don't know what the problem is but audio is unusable in Windows with any sound card (ISA or PCI) and any video card (PCI or AGP). In Windows 98, it stutters badly every time the screen is refreshed, and in Windows 2000, the machine simply freezes when trying to play audio (with any audio card). I tried ESS ES1869, Aztech WaveRider 32 (both ISA) and TerraTec Aureon 5.1 Fun (PCI).
No such problems with GA-5AX which seems to be a remarkably stable board overall. I had some issues with registry corruption in Windows 98 when using ALi drivers, but it's rock solid when using built-in drivers from Windows 98.
Another quirk of GA-5AX rev 4.1 is that it's kinda slow with PCI graphics cards.
E. g. in DOS Quake I get about 26 fps in timedemo1 in 640x480 using GeForce 2MX PCI, but I get 35.6 fps with GeForce 2MX AGP (both with write combine enabled).
VIA MVP3 seems to be stable with PCI graphics, but ALi Aladdin V seems to be faster with AGP graphics. Go figure.