MS-DOS Compatability Mode

My wife tried to install Leisure Suit Larry, an MS-DOS based video game, and could not get it to work. Sometime after that she noticed that the CD-ROM would not work. Upon further investigation I found that Windows was running in MS-DOS Compatability mode. She is running Windows 98 and I cannot get it to recognize the CD-ROM even with a boot disk. I tried to REM out the lines in the config.sys and the autoexec.bat files and it still didn’t recognize it. I have a 20GB drive with 2 partitions 10GB each and both partitions are running in Compatability Mode (apparently she tried to install it twice, once on each partition). There are no errors in the device manager that I can see. Help!