My two girls are sick again.

We started on the baytril/doxycycline almost 2 weeks ago - the sneezing and congestedness has been coming back - off and on - for about 2 days now. I called the vet and he says since they are still eating/drinking, and active, he wants to wait till after the girls finish their medicine and see if the symptoms get worse.
We're both puzzled. They've been "sick" (sneezing, congested) since mid-July, and despite the numerous meds they've been on, we can't seem to kick it. Any ideas??? They're on recycled paper bedding, have a huge cage with plenty of ventilation, and there's a vaporizer in their (my) room. I've run out of ideas... Help?
~Lauren~
Macie and Emma