For the morbidly curious, this is the (now corrected) code:

(defun jrl-collect-data (table input output)
  "Collect table data into lists of outputs per input"
  (let (res record in-val out-val collection)
    (while table
      (setq record (car table)
            in-val (assoc input record)
            out-val (assoc output record))
      (when (and in-val out-val)
        (pop in-val)
        (pop out-val)
        (setq collection (assoc in-val res))
        (if collection
            (push out-val (cdr collection))
          (push (list in-val out-val) res)))
      (pop table))
    res))

I should probably throw some comments in here, but essentially the assoc in the when block always returns nil on the first iteration of the loop, and if it can't progress past that point, it'll always return nil on subsequent loops and nothing will ever happen. As a result, any list I might feed into this function is always going to result in a nil output.