It could be a problem with the busmaster controller. It is possible that a previous failure to initialise the hard disk controller properly has caused windows to place an entry in the Registry, preventing it from trying to initialise the driver in the future. If you have W98 load the windows 98 CD Rom and in explorer navigate to the TOOLS\MTSUTIL folder on it. Right click the file named noide.inf file and select install. Restart the computer, and it should come back.
Is the Seagate drive the D drive, I had a similar problem when I installed a 2nd seagate. It was to do with the formatting, I will look through all my bits of paper to see if I can find out how I sorted it.