Had a similar problem on a BE6-2 with Win2K not remembering to make my TDK121032 (Plextor clone) use DMA even though "use it if available" was checked in device manager.
I found a registry hack (posted at the end of the message) in a Usenet post that worked. In this hack, it's assumed that the drive you want to run in DMA is set up as the Master on the Secondary IDE controller, so the keys with "Master" in them are the ones you want to look at if you intend to modify this. And note that this is for the Plextor 1210A and its clones. I don't know if it would work for other drives. Always export any registry keys to a file to back them up before you start hacking.
Anyway, with my TDK as the master on the secondary channel, I only had to make the following 3 changes in [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0002]:
"MasterDeviceTimingMode"=dword:00000410
"MasterDeviceTimingModeAllowed"=dword:ffffffff
"MasterIdDataCheckSum"=dword:00011cb8
After changing the registry, Device Manager immediately reported the drive was running in DMA mode but I had to reboot to make the change really work. Some have speculated that Win2K will switch the IDE channel from DMA to PIO if the system goes into suspend mode, so that's something to watch out for.
Here's the complete reg fix as posted on Usenet:
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0002]
"EnumPropPages32"="storprop.dll,IdePropPageProvider"
"InfPath"="mshdc.inf"
"InfSection"="atapi_Inst_secondary"
"ProviderName"="Microsoft"
"DriverDateData"=hex:00,c0,ff,a5,5c,d6,bf,01
"DriverDate"="6-15-2000"
"DriverVersion"="5.0.2195.0"
"MatchingDeviceId"="secondary_ide_channel"
"DriverDesc"="Secondary IDE Channel"
"MasterDeviceType"=dword:00000002
"SlaveDeviceType"=dword:00000002
"MasterDeviceTimingMode"=dword:00000410
"MasterIdDataCheckSum"=dword:000223da
"SlaveDeviceTimingMode"=dword:00000010
"SlaveIdDataCheckSum"=dword:00011cb8
"UserMasterDeviceTimingModeAllowed"=dword:ffffffff
"UserSlaveDeviceTimingModeAllowed"=dword:0000001f
"MasterDeviceTimingModeAllowed"=dword:ffffffff
"SlaveDeviceTimingModeAllowed"=dword:ffffffff