What is this?

My best guess would be that you are getting some sort of muscle cramp or muscle spam of one of the small muscles in the foot that is attached to the great toe and that spam pulls the toe under the second toe.

The plantarflexed 'pointed' position that the foot gets into during swimming might be what is triggering it.

The best you can do for it is what you are doing - massage.

I not sure there is much you can do about it

(I did have a patient with a similar problem, but it was brought on by sleeping face down; the position of the foot (combined with weight of bed covers) put the foot in a plantarflexed/pointed position and triggered a muscle spasm)

 

Well said, Mr.Craig Payne. My thought too. Most probably spasm, from the looks of it. A form of arthritis also manifests with the big toe seemingly going under the second toe (but actually, it's the second toe going above the big toe), but it's unlikely that you have this for a couple of reasons. One of which is that you're still quite young to have that manifestation of arthritis. Even though there's juvenile arthritis, it's still too early to have something manifest as that. Another reason is that bunions or arthritis will have the big toe go under the second toe consistently, not triggered by any stimulus, just automatically, AND usually without pain.

Moreover, that's why it's really likely a spasm is that it gets back to normal after stepping, bearing weight on it, and walking. Yes it hurts initially because you're stretching the contracting muscles, but at the same time, you're actively putting the tissues back onto their normal positions.

So that's my take on it. Prevention, I guess check the alignment of your foot and toes and check for equality in strength of all the structures. Check if your new shoes are causing some form of malalignment, and keep on doing stretches before exercises.