Windows real mode issues

I am working on a HD upgrade from 3 gig to 13 gig. the system bios seems to recognize it just fine. Windows 98 v4.1.1998 boots in safe mode, but will only boot normal if I check the force compatibility box in the system configuration tool. In this mode I have no cdroms and errors on my IDE controllers. Can anyone help me straiten this out without getting a different version of Win98?