i would clean the bubbler res. and add a bit of hydrogen peroxide to the solution when refilling. i had a similar problem and it seemed to clear up after i did this, how do the roots look? are they white and healthy looking? i would also gently rinse the roots in said solution before replacing it in the bubbler.
sounds like you got a good grip on the situation, and it`s no problem for me to try and help. remember, there no such thing as a stupid question, so fire away,i`ll do my best to help rectify any problem you may be having.