If you have not enabled floppy seek in the BIOS, enable it.
What you need to do is "stall" for time during the reboot for the drive to come up to speed to be detected. Any delay in the boot sequence that you can add, that runs before it tries to find the drive could help.
Although, I must admit that the problem usually happens during a cold rather than a warm boot if this is the cause.
I have been using a Western Digital WD1200JB 120 Gb hard drive as the boot drive on a system running Win98SE. The mobo is an ABIT VH7T. Recently the drive has been behaving oddly. If I perform a warm reboot using "restart", the BIOS fails to detect the drive and I get a "Failed Boot" error. If I restart and open the BIOS and highlight the drive location, "Auto" does find the Drive and I save the BIOS configuration and the system successfully reboots. The BIOS never fails to detect the drive if the PC is restarted from a cold boot when the system has been powered off and then restarted.
There is an additional drive (IBM 49Gb)attached to the same IDE port as a slave and it has never given any problem at all.
Neither Norton Disk Doctor nor the Western Digital Diagnostic tools detect any problem with the device.
I would appreciate any ideas anyone can provide on troubleshooting this issue.