Hey Jeremy,
To preface this, I do not have a good solution to your problem, unfortunately. Hopefully a better answer gets posted on this ASAP. I have not heard of this problem occurring, but something similar has happened to me.
I had a similar incident with my iPhone 5 a few months back. It could record voice memos, but would not register my voice when I made phone calls. Even weirder it would not play back voice memos and the headphone jack stopped working, altogether. I took it into Apple and was (get this) 6 days late for them to replace it.
I tried replacing so many things, to the point that I swapped my lobo into a completely different device. Turned out it was something on the logic board. Saddest of days.
The summary of this is that I would recommend swapping your customer's logic board into a working device (if you have a bench or some sort of working 5s). That will at least eliminate logic board as the cause. If the lobo works in the new device, start swapping out individual components until something seems to fix it. Check grounding clips, both microphones, and of course the proximity sensor.
Best of luck!
Jake