Sounds like a software problem to me. it is possible that something has become corrupted or is missing from your sys partition. When you boot off of the floppy and CD the file in question is more than likely being loaded into memory, thus it survives the warm reboot that you are doing.
After you boot up the next time you might try copying your current system to another partition or make a drawer and copy it into it you only have one partition, and reinstall your system over what you now have. If this straightens everything out great, if not you can always boot from the floppy and CD again and copy you sys back over as it was. If it does work you can compare the two systems and copy back newer llibs, etc.
If this doesn't work keep the copy of your sys and try new install. If this works you can do the same thing by copying back over newer libs, etc. a few at a time to see if you encounter a problem. If you do, you should be able to figure out what is causing it.
This is what I would do myself if this continued, and thankfully reinstalling the AmigaOS is a breeze compared to any other that I have ever seen.
regards,
