If I'm understanding correctly... You're rinsing the bottles after drinking, storing, rinsing, and sanitizing? I'd add another step here between rinses. Actually I'd eliminate the second rinse if your bottles aren't exposed to dust. But once you gather about a case of dirty bottles (bottles that have been rinsed after drinking), you should give them a nice soak in some oxiclean over night. Then rinse, dry, and stash in the "clean" stack of bottles. Then hit them again with starsan before bottling.
I'm going to probably say your infection occurred in the bottles.