I know this problem to well. Sometimes the Regimen is not powerful enough to deal with hormones. I unfortunately get 2-3 spots a few days before my period. Luckily I know enough when to expect it and make sure I have my AHA on hand to spot treat as soon as I feel it coming. I try yo do it morning and night to make sure it dries out the spot and it doesn't cause any red marks.
I went through the same thing. The Regimen is initially a very uncomfortable process for some to start out and there are days when it is very up and down. There are days your skin feels nice, and times when it doesn't. If it feels very uncomfortable try fanning your face or applying more moisturizer throughout the day or stick your face in the freezer for a few seconds...I used to do that a lot. But really, its only the 2nd week, it is too early to tell. I almost quit but I am so happy I didn't because I got clear and have stayed clear for almost 3 years now.