Just to be sure, I dont know what you know, so dont be insulted.....
You must install 98 before 2000, and the partitions must be formatted as fat32.
Now, its quite likely that there is either a software conflict or a hardware conflict, more likely to be software. If you have anti-virus software running, try either disabling it for testing purposes, or un-installing it altogether, Mcafee is notorious for causing these types of problems. Then move onto doing the same with other software youhave installed on your system.
For hardware, first update all your drivers, if you havent already, I.E. Video card, NIC or mdoem card, motherboard, soundcard, and whatever else you have in there. This will go a long way to ensuring you have a steady system. Also just check in the device manager to see if it is registering any hardware conflicts, (this is noted in the device manager be a little yellow exclamation mark beside the component in the list.) If it is you will have to change some settings like the IRQ that the conflicting pieces are using, but thats another question :-)
A final word about hardware conflicts is this, and it could be your problem right here, your motherboard utilizes the VIA chipset, and if you are using any of NVidia's videocards I.E. GeForce series or TNT series, there is a known conflict that happens at least in 98. You will need to download the 4 in 1 driver update as well as the updated drivers for your video card you can read about this issue and download the drivers here....
http://www.viahardware.com/download/index.shtm
Well my friend, good luck!
directionseeker