When you say "reset the battery", does that mean you replaced it entirely or just pulled it out and stuck it back in when clearing the CMOS? Reason I ask, is you may want to think about replacing the battery altogether, even if just as just part of the process of elimination.
Also, check your boot sequence BIOS settings, specifically the halt errors, it's easy to overlook the "Halt on All Errors" setting. Also check the boot devices and boot order, verify/change the boot order to make the hard drive the 1st bot device, or maybe even disable the floppy seek especially if it seeks the "A" drive and then gives the error.
It could be a bad BIOS flash. You can try re-flashing the BIOS to an older version and see how the machine works. If the older BIOS version takes and the machine works fine, try flashing with the latest BIOS version and see if you get the same problems.