Sounds about right. You REALLY need to be sure that your reservoir is properly aerated at all time. Scrub the bubble stone with a toothbrush to get all the crud off it before you hook it back up again just in case it's clogged. Check your lines for obstructions. Technically what you are doing is called DWC and there is a lot of good info for you in the hydro section.
You'll want to treat with peroxide. Look up threads about slime on roots in DWC- I think there are a couple kicking around somewhere.