Sounds obvious that something is bothering him. Does this happen a lot like every time you put him in that tub?
I think the problem might be that that tub contains some chemicals that are coming off in the water. Or maybe somethings in his eye or something like that. If its a recurring problem then keep reading.
I had my 2 RES in a rubber maid and put them in the sun for the summer (water and basking outside). However they would always act strange and simply stay underwater! I changed tanks and they basked in the sun and looked normal. I put them back in the rubbermaid the next day because that one is bigger and most suitable.. but again they just kept under the water. Eyes open, sometimes closed.
So I figure the problem I was having was that the rubbermaid had some type of chemical causing the water to be chlorine like. It even smelled like chlorine pool water if I went close to it. And thats strange because I rinsed the hell out of the container. I figure your problem may be similar.. chlorine water (or just salt content in water) isn't good for a turltes eyes and sometimes they may act that way by trying to rub their eyes.. with I'd say their Paw not their foot like you said. If a turtle could reach his foot to his eyes, well get that on national enquierer. So maybe change the container or simply really wash the container with dish washing soap and stuff like that. Give it a try
-just to add another thing, make sure the water you put your turtle in isn't very different temperature from what it has been in. Going from 75 degrees to 55 degrees is NOT good.. of course you may be keeping the water luke warm which is good, but just adding that since I don't know