WEKA Random Forest and numerical attributes
Weka does use its own implementation of C4.5, named J48.

That said, its RandomForest calls on RandomTree, which appears to be implemented independently, not ever touching the J48 code.  (That's from what I can tell, and I don't normally work in Java so take it with a grain of salt.)  I can't tell from a glance whether there are substantial differences aside from the obvious (that RandomTree subsets features available to split on at each node).

Class hierarchy of module tree
tree folder of source
(click through to see J48, RandomForest, RandomTree, etc.)