Windows 98 forced compatibility mode

I have unique situation. I am running an Acer Altos 500 server with scsi hard drive, running Windows 98 as the OS. ( I know..but dos apps need it) Had a recent corruption of Windows files, and it would not boot, it would only get as far as the Windows splash screen. So formatted, and trying to reinstall W98, but always hangs at splash screen I think at hardware detection. I disabled everything in startup, and still hung. When I forced compatibility mode, it finally completed the Windows installation. So I reselected all the startup options, and it booted fine, but now no CDrom. I unchecked the forced compatibility, and now it will not boot again. Anyone know what the heck is going on here?
Thanks,
Lor