Within the program editor, F3 is supposed to submit the active program or, if you have selected a subset of lines, it submits the selected lines. But it's possible that if you've got another window "active", even though the program lines are visible/selected, EG intercepts the F3 key and submits the active flow.
There isn't a way to change the F3 mapping for the entire app, so I think that for now you'll just have to be careful about what the active window is when you press it.
Chris
Become an Explorer! Join SAS Analytics Explorers to learn and complete challenges that earn rewards!