First off clean that bitch out real good with 10% bleach and hot tap water. Check any air hoses, pump parts, sprayers, and power wire for slime. Wipe them down and rinse with hot water. There's gotta be some there if it's on the stems. Wipe off the stems as best you can with a saturated bleach wipe or paper towels. Drain and wipe out out the res with the bleach solution and rinse well with steaming hot water.
Refill with cold tap water only. No clonex no hygozyme no h2o2. Use a timer for the pump that can be set to 1 min increments and set it to 1 min on 5 mins off. This will help keep the pump and water cool. Low temps will grow less bacteria. Keep your clone area at room temp or lower; not easy in warmer months I know. Drop a frozen water bottle in the reservoir everyday or twice daily if it's hot in there to keep temps down if needed.
Change out the tap water and wipe everything down with bleach solution or saturated bleach wipes once per week. It's easier to maintain through prevention than it is to treat once bacteria has set in.
The minute you see white roots emerging transplant directly to soil. Dipping the young roots in aloe gel and then granular mycorrhizae at transplants gets them off to a roaring start.