Hi Margot, I had somewhat the same problem on my 'off' foot the second time around. I developed a very painful spot just behind the second toe, at the joint and slightly behind it. It happened about three months into my recuperation, and may have been tied to an exercise I did, but also may just have happened.
I tried walking it out, but it got worse over time, I'd say it lasted a good seven months. About three months into having that pain, I went to a podiatrist, and he told me that in a normal gait, the pressure is put either on the outside edge of the foot, or on the inside edge of the foot; for some reason I was putting pressure on the middle of the foot - apparently a no-no for good walking. The extra pressure seems to have irritated the metatarsal area and actually caused thickening of the bone in the joint, causing at least some of the pain.
The podiatrist took my whole story in and said that he was going to treat me with anti-inflammatories to calm the joint down, then for long term, he suggested good inserts and to make sure I wear better shoes, preferably sneakers for the next month or so.
I did as he requested, and got better, but the pain did not totally go away until I started using these great new hiking boots that I got for the winter. Those and the inserts seemed to make all of the difference, with the pain pretty much gone now. I think it forced my gait to be corrected, so I wear them all of the time and am on a mission to replace my footwear with the best possible for what I do.
I think in recuperating, we tend to forget that shoes are capable of skewing your walk and causing issues.