I have a hunch, which I won't be able to confirm for a few days. The above behavior was observed on my brother's cab/Pi, which is identical to mine except that his IPAC is newer. I've read elsewhere that newer IPACs get recognized by retroarch as a USB gamepad and thus don't necessarily send the corresponding key.

On my machine, which has an IPAC that I bought in 2001 or 2002, everything shows up as a keypress, and the above behavior isn't an issue.

I'm going to see if I can retroarch to ignore the IPAC and just treat it as a keyboard so that we can share config without remapping. Otherwise, I might have to remap and get used to a different default layout. This is the layout I prefer, as it makes sense to me in ES, mame, and console emus:

(A/B1) (B/B2) (Y/B3)
(X/B4) (L/B5) (R/B6)