Anyway, after I installed, the D: (where XP was) was NTFS. I then formatted the E: (blank) to NTFS also. Then I tried to format the C: (Where 98SE still was). No luck. Windows said it couldn't do it (after I'd waited the whole time for it to actually happen). So I went into th C: and deleted all the files, set hidden files to be viewed, and there weren't any. I tried to format it to NTFS again. Same thing. I opened command prompt, and accessed the C: that way. I typed dir and found there were 2 files there, so I deleted them. When I tried to format, I got the exact same message.
When I checked the properties of the C: there was 335mb used. So I tried disk cleanup, and removed like 50mb of that from the recycle bin?
Still no format.
I've even tried formatting through command prompt. It says it can't unless I dismount the drive, so I dismount it, and then it goes ahead with the 'format'. But it doesn't actually do anything.
This partition is only about 3gb in side, so I can live without it, it's just annoying because on startup it asks if I want to start 'Microsoft Windows XP Professional' or 'Microsoft Windows'.