Previous posts have given some really good input...
A few years ago I had easy access to the cons skate range shoes through a freind, this was before the nike takeover, but they gad really great shoes with amazing suede (especially the CTS!) but my biggest problem with them was the insole, they simply didn't cut it. Being the idiot I was back then I somewhat ignored the pain, till one day I apparently fracture two bones in my feet & did significant nerve damage on my pushing leg.
After a long stint off the board and a couple of extra pounds gained, I tried skating again and started to feel the similar feeling in my foot as before, so I tried many different options on innersoles & shoes. I eventually found that janoskis actually work for me best once I wear them in a little bit and change to a rather thin ortho innersole, but I will say that certian innersoles are simply not meant to placed in certain shoes, I think someone already nailed it before mentioning about different thickness's/height's of the soles in particualar shoes...
Anyway the point I'm trying to make is Do not ignore it, start trying out different types of combinations and see what works best for you, if you still can't work it out, go see a doctor.