How to fix a stubborn windows keyboard?

I am running WinSE and it is on the primary FAT32 partition with 3 additional FAT32 partitions on my computer. I have been having an issue that has
got me and everyone else I've asked, stumped. I'd like to resolve this so i can use my keyboard again!
Recently I reformatted and reinstall the OS and all programs and it worked fine after this clean install for maybe a week before my keyboard started acting up. Now it only works SOMETIMES. I have to reboot like 3-9 times to get the darn thingto work in Windows98 BUT it always works in DOS. I know this cause I have a BIOS password set up, and I can type it in on bootup every time, AND I can press the F8 key BEFORE Win98 loads up everytime to get to the Win98 startup menu and use the arrows keys to scroll through. But once I am in windows, forget it. The keyboard wont respond, the caps lock and numlock lights wont even respond when I press them in Win98. I havent changed my keyboard, it is using the standard keyboard driver in Win98 like it was the last time (and i have had Win98 on this same computer previously for years with no probs with the keyboard). After I reboot a few times and Win98 finally lets me type I have NO problems using my KB until I shutdown to go to bed or leave, etc. Then I have a problem the next time I start my comp and have to continually reboot over and over into Windows til I can get use out of my keyboard. That is a pain in the butt! My mind is fried on this one.
I know if the keyboard didnt respond in DOS it would be a matter of just replacing the keyboard. I also know if that second KB didnt work maybe my motherboard's keyboard connector (or even the motherboard itself) would be at fault. But since I
can use this KB in DOS and in windows 98 after a coiuple of reboots, I doubt it is bad... My keyboard is only 3 years old, so I don't know what to do...

Please help!!