Here's one reason interest based ads might really affect your CTR.
A lot of traffic on my sites comes at "lunch hour". Surfers taking their first real break from work and wanting to get some serious PERSONAL shopping done. BUT, where are they? They're still at work. They've been using the internet for hours investigating WORK related topics.
But now they want to shop for personal items. But what ads are showing? Boring work related interest ads!
SO no clicks!
If Adsense allowed a geo-located timer control on interest based ads such that they would turn off or reset at lunch hour, then maybe they would work. Until then I leave them OFF!
Go to your "My Account" Tab and turn them off, maybe it will help!