If you are pasteurizing and are having contamination issues, it's time for a full audit of your downstream equipment and workflow in the process.
Identify every piece of equipment, and try to identify possible sources of contamination.... for example, are there scratches on any of the handling equipment? How about the vat? Is there any biofilm that has built up? For your air, have you changed the filter and the area around it? Are you possibly bringing this in from the outside? Changing clothes when you come in, wearing protective gear? Probably not the latter if you're doing 3 gal batches, but similar idea applies. Somewhere, you have a failure in equipment, in cleaning and sanitization, or there is something transferred through the air or through contact.
Also look at your sterilization schedule. Yes, technically boiling helps, but I have seen biofilm issues that boiling does not solve. It's more effective to use at least a 150 ppm chlorine rinse to sanitize, after a caustic/detergent wash to clean.