I just want to clarify a couple things to help in the diagnosis. When you copied the database to another directory, was it able to do that successfully? If so, it doesn't sound like the actual database is corrupt. PcTools used to have a utility that would check the drive for errors. Did you try that?

I'm assuming you're running Pkzip in order to make the database small enough to copy to a floppy. I'm wondering if Pkzip is putting the temporary file it creates in a corrupt spot. I can't remember if you have a way of forcing where it creates its zipped file. Possibly, it could put the file directly on a floppy.

Another thought is that Pkzip is running out of memory (RAM) creating the file. You might need to run a memory manager, if one is available. Pctools used to have one of those, if I recall correctly. 

In the end, it might be just as simple to physically put the whole drive in a modern computer and let Windows do the work of accessing the drive and copying the files. You can use the same cable as the dvd/cdrom drive. I'm not sure if the bios on a modern computer would automatically recognize the drive or not.