Have the new cranks maybe changed this? Square taper <-> pedal width varies between cranks; I had a pretty big increase in width after changing mine before I realised and fixed it with a shorter BB.
My thoughts exactly. Will have a measuring session and find out.
Can you try and fiddle the boom out a bit further?
Yeah, I'll play with that when I get some proper 'bent-riding weather. I don't really want to take it out when there's salty slush about, as it's just had a nice new chain and is generally a bugger to clean.
You've probably tried this already and I've forgotten, but have you explored fiddling cleat angle to try more heel in/outward angles?
I've been experimenting with cleat positions on the other bike. I put them back to the original position to see what difference, if any, the short cranks would make. So far it seems that having the cleats further forward, and with the left cleat further forward than the right, is helpful.
I've played with angles in the past, and know that my right knee wants to be pretty much straight on otherwise the *other* knee problem manifests (in fact, my main reason for using clipless pedals is that it stops me from twisting the heel inwards, which b0rks the front of my knee in short order). Physiotherapist agrees that this is the Right Thing.
Since things are consistently worse on the 'bent, I think my best approach at this point is trying to determine what's different there.