Well, first thing to check is that the bindkeys for Enter and double click left mouse are set, but assuming they are, I suspect it's probably because you're not using a ?doneProc with enterPoints and have "Repeat Commands" set in the Options->Editor form.
If Repeat Commands is enabled, then the enterPoints() function does not return after you've hit the return key or double-clicked - instead, it goes back to the "first" prompt again and asks again. Since the expected use model with an enterFunction is to use the ?doneProc callback to do the action, this makes sense - as it allows you to repeatedly do the same thing over and over again.
You can observe this by doing:
procedure(MyDoneProc(win ok points) printf("FINISHED: %L %L\n" ok points))
enterPoints(?prompts '("first" "next") ?doneProc "MyDoneProc")
You should see the "FINISHED" message when you hit return or double click. Is that happening? Also, the prompt will go back to "first" rather than "next". Then also try turning off Repeat Commands and see what happens.