Strange contamination - (Oct/14/2014 )

Dear all researchers, 

I am facing a mysterious testing results recently. I was collected sample of probiotic culture from a large fermenter tank into 100mL lab bottle under sterile condition, the sample was subjected for E.coli testing and showed positive result in MacConkey broth. However, when the same culture collected from the same tank next day into another lab bottle was showed negative result in MacConkey broth. The same problem happened for almost 2 months. 

May I know did anyone experience it before or anyone have any idea why it is happening? 

Low level contamination? Perhaps the E coli are being out-competed or inhibited/killed by the rest of the culture? Perhaps your MacConkey has a contaminant in it, or the plates you are using are suspect?