I am a little late in the response here, but I will reply anyway:
Surely it would seem more likely that the flag was put there as the traditional explanation goes, in the 60s, and it would seem less likely that the govt lied about putting it there in the 60s but then realised they had to get a flag there afterwards so sent up a new secret mission? And all the while the astronomers be it professional or amateur who observed the site at the time didn't notice this strange new flag pop up some time after the 60s?
I mean I guess it is possible that they sent up an unmanned mission instead of a manned mission at the time they said they did, but if you're already going to such an expense why not just put some people inside and call it a day lol.
I get that the govt lies about many things (eg NSA etc) but it seems that this would be a pretty trivial thing to lie about, at least for such a sustained period of time.