lkrd - It would probably have been more benificial for you to apply once your masters was complete....however in my opinion if you get accepted on to an air traffic control course, why would you need a masters? Is it not a career for life?
I'm sure an e-mail to HR will answer your question anyway - I have read on here before they seem to be pretty lienent with dates. You might get lucky, however like I say - if I'm allocated a course,I'd drop everything to get started right away...no delays.