If it's Vista you're running (could also happen in Windows 7 as well), the emulator causes the PC to have to auto change resolutions, but it usually happens quick and takes about a minute or so to let the change happen and for you to be able to do anything. But I don't have issues with anything freezing with Kega Fusion, not even with 6 Firefox tabs open and Chrome open as well. Try a fresher or older version of Kega Fusion and see if the same thing happens, if so, you could have deeper issues than just some emulator causing freezing issues (I'm not tech savvy to be able to say what the issues may be, someone else could come along and help out).