As I suspected, the in-circuit serial programming problem I was having with the new Ifos prototypes was due to a lack of isolation between the ICSP interface and the rest of the Ifos circuit. Not sure how the breadboard prototypes work in spite of this, but the circuit-board-based versions are definitely affected. Here's the original circuit:
It was easily corrected with a few cut traces, a bit of green wire, and a single 1N914 diode. The practical fix isn't very pretty (photo omitted to maintain illusion of soldering competence), but it works fine. If this design ever goes through another manufacturing run, here are the relevant changes I'll have to make:
The real question is, "Should I even bother with ICSP in future versions?" A bootloader would certainly simplify the hardware and update process. I've been weighing the various pros and cons for a while; the question probably warrants a separate post at some point.