Are you saving the changes in BIOS before you exit?
Found this ages ago when i was having trouble with a format its a bit long winded but worked!
You will need a win98 start up disk if you dont have one go to
www.bootdisc.com & download one on to a floppy .
Insert the floppy in the pc & boot up.
Choose option WITH CD ROM SUPPORT
At the a:prompt type in Fdisk . You then get a message do you want to continue with large disk support press enter .
You then get 4 choices enter choice 3 Delete partition .
then enter choice 4 delete non dos partition .
Just follow the instructions it will tell you it is deleted .
Then you must create a new partition.
On th FDISK menu choose option 1 create a primary dos partition & just folow the instructions .
When you have finished press ESC to get back to a: prompt.
Leave the win 98 start up disc in reboot ( press control , alt & delete ) .
This time take choice 1 With cd rom support .
At the a: prompt type in FORMAT C:/S this makes the drive bootable & puts system file on . it will take about 10 min there is a %progress bar.
When it is finished at the a; prompt Type in D: if D:IS YOUR CDROM DRIVE .
Put in your WIN98 CD
At the D: prompt type in SETUP
Then it is just a case of following the WIN98 CD SET
hope it helps