Like most things in life, Eclipse (which ColdFusion Builder is built on) can do with a clean every now and then. Generally I find after upgrades, installs or if you are seeing performance issues, the first thing to do is give it a clean. And, while there, make sure you get behind the ears, scrub the feet, etc.
Fortunately it is pretty easy to give Eclipse a good clean — and without getting your computer wet. Just follow these instructions.