I always have foot pain for my first 2 or 3 runs, but it almost always goes away. I feel like this probably due to the fact that I don't get to ride as much as I'd like, so those foot muscles are just weak-sauce.
Anyways, I have noticed that adjusting my boots can make a difference in the severity and duration of this pain. I ride Burton Ruler boots with Cartel bindings. I switched out the Burton insoles for Shred Soles, which has been pretty helpful so far. I also have started making my liner pretty snug, and my outer laces a little looser. This combo has really reduced the pain for me, but YMMV.