Follow-up: I had a very nice phone call today from a friendly person in Alaska MP customer care, who readily offered to refund my miles and fees, plus a little extra dollop of miles for my trouble.

She had been able to access my record and saw that on the day I put the redemption through last year, I was sent four different email confirmations at different hours, each presenting a new, different calculation of taxes and fees. (Now I remember.) The trail suggests someone on the partner desk pulled the booking and worked on it manually, miscalculating the partner booking fee (first subtracting it, then doubling it, etc.) and in so doing may have led EI to think it was not paid properly, or only half-paid. (Although why EI would display the res as intact on its own system, and even happily assign two seats, is a mystery.)

I must have seen all those emails as they flew by, but concluded that as long as I ended up paying the proper amount, no problem. Wrong. Somewhere along the line the booking was corrupted, with all those varying confirmations the only outward sign. Lesson learned: any anomalous communication from the airline, even the automated kind, is grounds for calling in. But to AS' credit they owned it in this case.