In case anyone else comes here and have this problem: this is an issue with KSP, Parallax and lights. Nothing to do with Waterfall.
You can easily replicate this by driving a rover with many lights (stock Crater Crawler works well) around the space center and turning on the lights. With Parallax installed the FPS will immediately tank and then recover when you turn off the lights.
If you want to use both Parallax and Waterfall you can disable the per pixel lighting in Waterfall and the FPS will no longer drop on launch. You'll probably still have issues if you turn on any other lights when on the surface though.