i ordered the Server 2003 Enterprise edition a few weeks ago.i recieved it and went to install wen it siad you cannot upgrade from 98.i fort arrrr.so i cliked ok or summin and a box came up saying which install you would want to make.bean was confused(i am bean!)so i cliked install and it started installing..weird.but i had 98 so i odnt know how...and..cause it did..would the be any files missing?
i dont know y there shuld be but there might ;) :rtfm:

you can't upgrade from windows 98 to windows server 2003. it just started to proceed with a new installation. that's all. ;)

Don't put Server 2003 on the same partition as Win 98. Put Win 98 on C: and Server 2003 on any other partition and you'll be fine. And you can boot into the one you want from the boot menu at startup. Always install win 98 first as it'll overwrite the Server 2003 boot menu loader.