Steps to reproduce:
Load a file that has clojure highlighting, with
let g:clj_paren_rainbow=1 in the .vimrc. Observe the rainbow parentheses. Change the colorscheme to another color, and the rainbow highlighting goes away. Changing the colorscheme back to the original color does not restore the rainbows. If I then say ":set syntax=clojure", rainbows are restored.
What I expected: When I change the colorscheme, the rainbow effects do not change. If there was a problem with the other colorscheme, changing back might have restored the rainbows, but it seems like something else is going on.