yes, i hear it takes a few weeks for the meds to properly address the serotonin issues that are causing these things, and that you end up feeling worse before you feel better, but hang in there hon ... it WILL kick in, and you WILL start to feel better, and if it doesn't kick in by week 3 or whenever your pdoc told you it would, be sure to call and report in to him or her.
what you're describing sounds just like what my mate described about his -- he too was able to "know" the thoughts were irrational, etc. but he too could not stop them or stop himself from obsessing on them or acting on them. it's not your fault; it is something you can't control right now. just hang on till the meds have a chance to work. and keep on posting here if it helps ease the stress for you to just talk about it in a safe environment.