Also, why do you have shoes on half the year and not the other half? I get that in some places ground can be pretty bad, but I would think that overall changing from shoe to no shoe every year wouldn't be great for the horse, their hoof has enough time to grow tender and then you take the shoes of and they have to adjust their paces etc. I find that most horses, given time, can adjust to dealing almost all footings without shoes.
I had an ex racer, who was shod all his life, and then one shoeing a farrier cut him way too short. The next day he was laim, and we got a good farrier out and they told us that it would be best just to leave him for a few months, to outgrow everything. So we took his shoes off, didn't ride him for a few months, and after without shoes he was sounder than ever. Riding over rocks didn't bother him. My current horse has never had shoes on and she's fine.
It could be just him being a bit sore after a trim, but if he doesn't seem to get much better then maybe see if you can find a different farrier who is experienced in barefoot to come out and have a look.