A basking light to warm the basking area would be rather important now, as it is cooling down- chances are that a lot of the time his water is warmer than the air at the moment, so he doesn't want to leave the water- he has no incentive to bask and dry out, which is essential to main a healthy shell.
How big is the turtle? a 50 litre doesn't sound like much... Turtles produce huge amounts of waste, so often need very high filtration (With good biological filtration) and the smaller the volume of water, the more rapidly toxic substances from the turtles faeces, food debris etc. can build up. Typically external canister filters do the best job at filtering turtle tanks (so do sump filters) as they have a much larger volume so you can pack a heap of filter media in there, particularly biological media like ceramic rings- the biological media allows good bacterial growth on them, and these bacteria convert ammonia from wastes, breakdown products etc to less toxic nitrites, and then again to even more benign nitrates. Nitrates do still build up in the tank and can reach toxic levels so you still need to do regular partial water changes even with a powerful filter. The best way to monitor these is to buy test kits- they have them for a huge assortment of things- I use the ammonia, nitrite and nitrate test kits. Look up 'cycling fish tanks' and it will explain the process to you
When you do the water changes, do you change all of the water, or only a percentage of it? if so, about how much do you change?
For calcium, I often give my boy cuttlefish (the same type you give to birds)- just use a sharp knife to get the hard back off it and put chunks in the tank. My shortneck would just periodically eat bits of it. He also has access to fish and shrimp for a calcium source.
I'd kind of be inclined to think that it may be a water quality issue thats causing you problems, and probably the lack of effective basking (his/her shell isn't drying out sufficiently and regularly enough). Try posting on the other site listed above, those guys really know their stuff and may be able to help you out as well. I may be completely on the wrong track with what I've said, its kind of hard when you can't see the animal etc. I would still recommend a trip to a reptile vet if possible.
