I don't know when this happened, but it was broken already in 4.6a SR-2.
There used to be a panel menu in the Cited By Tool, where you could select which collections you wanted included in the results, as well as a bunch of other options (documented in the wiki).
Now there is no way to drop down that menu. The icon for it, which used to look like this:

now is just a triangle:

Clicking on it does nothing. The collections selected in the Cited By window are just whatever I had selected the last time this panel menu was working, and there's now no way to change them.
EDIT: It turns out not to be actually broken, but only appears broken due to three problems (which should be fixed or improved IMHO): an odd icon glitch, slow menu population, and no UI feedback while it is populating. See my second post further down the thread for further details.