If it's of any help in the future, Windows only needs a megabyte or two on the first primary partition it can see on hda. Autoexec.bat, Config.sys and a few others need to live there, but the Windows directory itself can be on a logical partition on another drive.I could wipe hdd and put nothing but windows stuff on it, if that would correct the problem. But some of windows would still need to be on hda. The main loss would be having the linux swap on a separate drive.
Yes, I have done it. I ran Win98 for some time from a logical partition on hdb, which didn't have any primaries. A small FAT primary on hda was the boot partition for at least three Windows versions.
-- Joe