I didn't have any issues at all. Not one. After receiving and accepting my FAA facility, my FAA HR rep asked for the contact information for my DoD HR rep. I sent an email with a cc: explaining I would be transferring from DoD to FAA with no break in service. Process was easy peasy from there.
Recommendation: If you have a start date and this hasn't happened for you, there's nothing wrong with being proactive and connecting the two HR reps.