Your feet will swell when you ride. It could be that for shorter rides there isn't enough time for them to swell significantly enough to bother you.

Another thing you could be experiencing are hot spots, which typically are felt where you describe your pain occurring. For your sake, I hope it's not it as I've experienced hot spots and they are maddening. If it is there are insoles that have a metatarsal button that can alleviate the pain. Specialized's inserts have the metatarsal button.

Another thing that is suggested for people who get hot spots is to try a very stiff carbon soled shoe. Obviously, it makes sense to try the inserts first.