I've found that you can get precisely one medal after the box appears. I just got FLAK Expert to round off my medal score at 10,000, but I did not get Master Tactician, which I somehow achieved after FLAK Expert (seriously, I have no idea how I got it; it just appeared). So my in-game achievements are complete, but I'm still shy 3 medals: the two 100 pointers, and the cutscene one (seriously, how many are there? I watched them all up to the 48 hour one, where they stopped, and got no love).
Incidentally, I'm up to 10,000 points. Not bad considering I haven't gotten any in Sonny 2 or the Doom trilogy. I just played a 138 hour game, my personal best. I know I said I wasn't going to play this game until the medals were fixed, but I just really wanted to get my score up to 10,000. And now I have. Good night.