I have the same problem before I understand what marlin/pronterface waiting.
I thing you reversing some millimeters (example: 20mm), and after you extruding 50mm for have some filament goes outside the nozzle. So I don't know if it's a marlin/pronterface waiting but when you push resume, I will immediatelly reverse 30mm of filament (50mm - 20mm).
So the solution for me was to reverse filament about 100mm (you can put less, but you need to do enougth empty reverse feed), and after put EXACTLY the same manuall extrude length. And HOURRA !!!! :-D
I hope you have understand what I say. And it's will work for you.