Hm... do you mean you have crampin? like as if a muscle in your foot is overlappin another one? You're better off doin seated ones first, then standin! Also check your sneakers out your foot has to have a arch, flat footed people dont have to worry cuz they've grown all their lives with flat feet. So they're able to do anythin stressfull and it wouldnt bug em at all.
I don't think this has to do with shoes. During my first month or 2 of doing calf work, I had the exact same problem, especially on the rotary calf machine. I suspect it was due to the fact that the tendons and ligaments of my feet weren't strong enough yet for heavy calf work. It went away pretty soon. I started to work out with a beginner friend last semester, and he complained about the exact same thing. It went away for him too.
Height - 5'10
Weight - 157 (cutting)
Age - 19
Dumbbell Bench - 55 x 7
Deadlift - 250 x 8
Squat - 170 x 6
I have to wear crosstrainers because I have very high arches and I get the same pain. It sometimes keeps me from doing em, I don't wanna deal with the foot pain. The only thing that seems to help after doing calf raises for me is a foot bath, that silly looking little electric foot massager. You can get em for under $20. It looks stupid, but it does wonders. Fill it with the hottest water you can stand and soak your feet for 15 mins, your feet will feel much better after your workout, no more pain. If you're lucky enough to have a jaccuzzi, you could use that too, put your feet near the jets.
I used to get a similar pain when I went running, I rested up for a few weeks then eased back into it more gradually and it went. It was kind of like a cramp pain right on the arch. The problem with feet is they never really get any rest because even when you're not execising on them you walk and stand on them all day long which means any injury there can be difficult to heal. I'd say ease down on whatever running/calf work you're doing then build up again more gradually and pay attention to the pain - it's there for a reason.
Waist 32" (a little bit under now!)
DL = 420lbs, BP = 280lbs, Squat = 345lbs