The natural cycle of ich is that it will appear to be gone, but then come back. You'll see the "salt granules" one day, and the next they'll be gone. That's what makes this parasite tough to treat if you don't stick to the treatment routine and think "Oh... it's gone, I don't need to do this anymore."
As CaptainAhab said, you need to do the hypo for 4 weeks AFTER you see the last spot. If you're two weeks in and it reappears, the clock starts over again.
Regarding the fish breathing hard, are you checking for ammonia? Removing all the rock might've taken a fair amount of your bacterial filtration out and you might be experiencing a little cycle?
Just make sure you keep the salinity at 1.009 - no more, no less - and if you haven't seen this link yet you might give it a read over:
ATJ's Marine Aquarium Site - Reference - Hyposalinity Treatment