Klonopin, like any other benzo drug, can slow down motility. I have IBS-C and take it, but the thing about benzos is that they stop working on the anxiety after a few months and you have to keep upping the dose to get an effect. When you try to get off them, you have to go through withdrawal.The worsening of your anxiety may be due to a sole reliance on medication as you build up a tolerance to it over time, so while Klonopin once helped you control your anxiety/stress and thus the IBS, it now has little or no effect. Try to wean yourself off the Klonopin with CBT and/or hypnotherapy. (I'm a fine one to talk as I've been addicted to benzos since I was 16 years old. I'm not off them entirely, but CBT and hypnotherapy have allowed me to decrease my dosage of Klonopin to a fraction of what I used to take. My goal is to get off of the stuff completely.)