According to the instructions, the capful of bleach was for the plastic bags. The clean water through the filter by backflushing is just design to push dirt out. When you use it in normal sense, all the crap gets stop by a filter. When you backflush it, it goes backwards and out. Least that way I interpret it. I'm just an accountant, my knowledge on bacteria and all is limited. I'm just using the instructions on the plastic bags the filter came with. I didn't use a single bleach for my previous filter. (Katadyn) I would take it a apart and use the scrubber it came with to scrub off excess crap that the filter has caught.

Edit: I forgot to clarify, if you backflush the filter after each use with, I think you will discourage any bacteria growth..Again, I'm just an accountant. I also figure even if there is bacteria in the filter the filter still suppose to stop it from getting in your drinking water.