When in doubt toss the floppy and cd rom option out!
In other words set the hard drive as the first in the order and disable the rest. This will force the system to llok at the hard drive and not an empty floppy or optical drive for boot information there.
If you have the zip drive on the primary ide cable while the hard drive is on the secondary ide channel that still shouldn't see Windows seeing itself as E however unless there was a disk in the zip drive while Windows was being installed and the installer tried to write mbr entries there. And that doesn't add up either.
Did you split the 640gb drive into different partitions at all? Windows going on a second or third partition would be the only thing to account for why Windows is seeing itself as E without another hard drive present.
Meanwhile the LBA or Logical Block Addressing should be enabled. Especially on older boards that allows support for larger capacity drives.