Interesting I stumbled upon this post. I just got off the phone with the head person over at my local FSDO, and posed this exact question.

I've got 1,380 total time with civ + 781 time in the military.....but I also keep a log book that I log my Mil time in from taxi-to-shutdown and that puts me at around 1,518 - so I asked what I should do, and she told me very definitively that my personal log book was what mattered.

It's an odd situation though, what would an airline think looking at an application with 1,380 in for the total time, but an unrestricted ATP??