Flukes do sound like they may be the issue Aaron.. But its going to take a prolonged treatment to deal with it if these are a problem....
You may want to consider using someing like quick cure(formalin malachite green) or just formalin... Treat every other day for several treatments..
Try upping the aeration as well.... If you are feeding heavy...they will breath heavy at this time and thereafter for a bit.
hth,
al