We're expecting RET to perform minibuffer-exit. That's the default keybinding from minibuffer-mode-map. Perhaps another keybinding (from another minor-mode keymap, say) is overriding the minibuffer's RET binding.
it just goes to the next line
Hmmm, this sounds familiar. I had this problem last year.
Do you have Paredit mode enabled in the minibuffer? (You might look at the value of eval-expression-minibuffer-setup-hook.)
The paredit-mode-map has the paredit-RET command bound to RET instead. This command usually puts a new line in place.