Win2k SP4

I am running Windows 2000 dual boot with Windows 98SE. My Windows 2000 is SP2. When SP3 came out I downloaded it and installed it with the option to uninstall if I needed to. After I installed it my computer would freeze up and I would have to manually shut it down. At the time I thought it might have been a bad download. When SP4 came out I ordered the CD and installed it first on two of my other computers with Win2k without a problem. But when I did it on this one once again I have this freezing problem. I had to uninstall SP4 and go back to SP2. Question: Does this have something to do with my computer being a dual boot?