Handbrake running extremely slow

What's your cpu? If it's one thing that depends on a cpu, it's video encoding.

My old G5 iMac ran at .05 fps for high profile x264 encodes, while a lynnfield can do the same talk at 80fps-- a 1600x increase for a cpu that's only 6 years newer.

Also do note that speeds while video encoding will vary greatly depending on what it's doing. If you're doing a 2 pass encode with filters, the first pass will breeze by, but once it gets to the second pass where it actually has to apply filters and allocate macroblocks by frame prediction, the fps of your encode will slow down tremendously; the same can be said for high movement scenes vs stationary scenes.