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Win98 second edition problems

said: I have updated from Win95 to 98SE and have problems with my CD Writer and with one major software program. In each case a warning box comes up saying, 'This program may not run properly in Win98 due to enhancements.....' The CD Writer works but with some anomalous results but the software program goes crazy. What are these 'enhancements' and is there any way around them? I have heard that IE5 is causing difficulties with some programs.