When you get to the BIOS setup, do you just reboot? Try checking all the info to see if it's correct, then using the Save and Exit option... there may just be something that has changed and the bios keeps trying to get you to update it.
But, with the wrong times on some files (is the computer clock still keeping correct time?), it might be the battery getting weak on the motherboard.
It could also be that removing certain programs has messed up the mbr (master boot record) of the harddrive, so the bios has trouble recognizing the HD and brings up the bios setup screen. Boot from a floppy bootup disk for win98... at the a:\ prompt, type "fdisk /mbr" (without the quote marks)... that will reset the mbr . Note: if you have any 3rd party boot loader or disk overlay installed, it will be gone, so use the mbr command with caution (there's no problem if you only have one os on the computer and the hard drive is not compressed)
But, I'd try the Save and Exit option first on the bios setup... it may just be asking you to ok a change that has been made. And the time changes sound suspiciously like a weak battery...
but then again, since the problem started when you removed some program, it could be the mbr needs reset, but at least read up on the mbr command before using it, because it can really mess up a hard drive if used improperly. There are some really scary stories online from people who aparently don't know nearly as much as the think they do, so, before doing a google search for "fdisk /mbr", read the actual facts on Microsoft's websitehttp://support.micro....com/kb/q69013/
it's very safe to use if done properly.