|Are you sure dos sees the drive? I don't understand how dos can see it but windows can't. Is it running in msdos compatibility mode?|
Anyway, if you copy the files in pure dos, such as booting directly into dos or exiting windows into dos, then as Derek says, it's going to copy them all in 8.3 format. But if you're in 98 and open up a dos window to do the copying, it'll copy them correctly.