As others have said, it probably started because of poor water conditions.
I realize you said it didn't have any nitrites in the tank, but a cycled tank will test with 0 Ammonia, 0 Nitrites, and some Nitrates. (Nitrates are essentially the end product of the bacterial cycle). Unfortunately, nothing takes the nitrates out of the water except plants and water changes.
Many people (myself included, before petfish.net), have the habit of just adding water to the tank as it evaporates... but this does nothing to remove the nitrates.
Nitrates are also harmful to the fish, and it is best to keep nitrates below about 20 ppm, I think.
Most likely, as others have said, the sore and lethargic behavior is a result of poor water quality, Doing such a thorough cleaning of the filter has removed or killed most of the bacteria and the bacterial colonies will need to become re-established.
Do frequent water changes as mollielover suggested to keep the toxin levels down while the tank cycles.
Or... do you have another established tank available? You can always add "filter squeezin's" from that tank to give it a bacterial boost.