I was initially setting my master and slave drives but when I rebooted the slave was not being recognized so I checked the IDE cable to see if there was an issue. I did this a couple of times only to find it was not working, I also got no OS on this drive a few times, this happened before but was easily remidied by simply adjusting the IDE cable. The last time I fixed the cable the master still was only being seen but when windows booted it crashed, thus setting off the events in my first post.

I got Warning windows has detected a registry/configuration error. Then whenever I booted it went directly to the safe mode/normal boot selection screen.Like This:
* Create a startup log file
* (Bootlog.txt)
* Enable SMARTDRV disk cache
* [Not sure what the name of this was but it was step by step process of Y/N. The questions where:
Loading and initializing
(FSHLP.SYS driver
Load all windows drivers

Which I assume would be normal but anytime I selected any of the above options I got the:
Registry file was not found. Registry services may be inoperative for this session. It would then shut itself off automatically. I also got these info once:
Override standard IFSMGR
Msmouse.vxd [Also when I changed the IDE cable both master and slave were recognized]

You might try this. With computer off, insert your start up disk and start the computer. It will boot and give you a screen to select start up mode, normal, safe, step by step, etc. chose the step by step and for 'each' entry, select Y for yes. Restart computer still with the disk in drive and let it reboot but this time, select either 'Start without CD support' or 'Minimal' and let it boot to the DOS prompt. At the prompt, type Scandisk /All (note the space between the k and the /) and if it finds any errors, select S for Save and skip undo. Then back at the DOS prompt, type in scanreg /fix. Your computer should restart automatically, but if not, restart it. Hope this helps. Good Luck.