Uni, all the caps (including those on the power supply) have been replaced with tants or ceramics (on motherboards) on both machines, so I'm thinking perhaps not the caps in this case.

Byrd, thanks for the suggestion - I'll see what I can do about that. The floppy cable (particularly for the Floppy Emu) works fine with other Macs, though maybe it's the floppy connectors on the motherboards for each problem machine. Perhaps it's a hard drive issue - maybe something to do with non-Apple HDDs? It must be said that I haven't had the issue with my Mac LC III, which uses the SCSI2SD converter. Also, my Mac IIx with stock HDD seems fine. Anyway...something for me to consider. Will update when possible and welcome any other suggestions.