Sounds EXACTLY like what happened to me last year. I noticed it when I was going through the trees in Big White... probably because I was always on my toes. I never really got it here since the runs are much shorter, but I had an issue out west. I even bought new boots out there and I still had issues. It was really bad to the point where id have to stop for 5 minutes or so. Eventually, I'd get through like 5 runs and it would get a little better.
This year I got back into rollerblading and I noticed the same pain. One thing that helped a bit for that was Dr. Sholls foot insoles (the athletic ones with the gel in them) I still get a bit of pain, but probably half of what I used to get. I think that in both cases, it was caused by vibrations on my foot (rollerblading on very smooth pavement was fine, the second I went onto an older road, I'd really feel it) I'm hoping that a new board with a damper ride will help me a bit this year, otherwise, i'll have to see a doctor.