i use starsan as a sanitizer and from what I know, it does not contain chlorine.
I am fairly meticulous when it comes to sanitizing, so I don't think that is the problem. I run starsan through my pump for 10 mins before I use it to transfer to the carboy. I am using a brutus system with two pumps, one is used for transferring from the mash only and the other for the wort only. I soak the carboys and tubing for a minimum of 20 mins before use.
Certainly infections could be the problem, I did just brew using bottled water instead of my tap water to see if the same issues develop as previous batches.