Most bacteria that grows in a system will not make you ill. Unless you have a system that is dispensed with air.
Draught systems require cleaning every two weeks to keep the bio level at which the flavor of the beer will not be changed. Possibly the disenfectant you are using is causing problems. Be certain to use a detergent and disenfectant designed for beer glasses. Always allow the disenfectant to dry off the glass before dispensing.
Scott Zuhse, Instructor
Micro Matic Dispense Institute