I really appreciate your help!
I have two I-O's both V5's with similar IDE DMA problems. One is a complicated machine with a hard drive and an IDE CDROM drive, which I won't describe since it is not a good base case. My second I-O is a V5 with the following:
Bios: 5.31c, also tried ver 5.30
CPU: AMD K6-2+ @ 400MHz
HDD: OEM IBM TravelStar 10 GB, also tried a Hitachi 15 GB drive
VIA: ver 4.38 4-in-1, also tried ver 4.35
San: Sandisk is disabled in bios (D: drive is "none"), but active electrically
PCI: pci.exe run in autoexec.bat with parameter set to 32, also tried w/o pci.exe
Mem: 128 MB
Op: Win 98 SE, clean install with all updates (IE 6.0, security patches, etc.)
My Trials: With ver 5.30 bios and Hitachi drive, and ver 4.35 4-in-1's, DMA box would not stay checked, but machine would reboot OK with no errors. With ver 5.31c bios, 4.35 or 4.38 4-in-1's and Hitachi drive, same behavior was observed. With ver 5.31c bios, no 4-in-1's (ie Microsoft via bus master in Win 98) and Hitachi drive, same thing.
The IBM drive is a different story! With ver 5.31c bios and Microsoft via bus master and IBM drive, checking DMA practically destroys the machine. Machine reboots in DOS compatibility mode on primary IDE and you can't do a thing to change this! You can't even install 4-in-1's. With ver 5.31c bios, ver 4.38 4-in-1's and IBM drive, same thing--DOS compatibility mode. At least in this case it is possible (with a lot of crashes) to get the 4-in-1's re-installed and out of DOS compatibility mode.
Now, I have of course set the machine up with primary IDE only to avoid the IRQ 15 conflict with USB (I note that installing the 4-in-1's re-enables the secondary IDE port and you have to turn it off again). I have also looked at my DMA controller in the System devices. It is working properly, and happily assigns DMA 3 to the parallel port if I set that port up for ECP mode.
The difference in behavior between the IBM and Hitachi drives suggests to me that the drive hardware microcode is a key to this mystery.
By the way, pci.exe speeds up IDE transfers significantly, even w/o DMA--from 2.8 to 6.4 MB/sec on the Hitachi, and from 2.9 to 8.3 MB/sec on the IBM drive! Thank you for pci.exe!