I'm playing the same kind of game I always play: passive diplomatic victory goal. Before the beta 1.1, I rarely saw that message. But I've seen it from three different civs in my first (only) beta game.
The only things I can think of would be a hypersensitivity of the AI to sudden military buildup or to influence starbases outside my own "territory". The first AI to "know what I'm doing" showed that message sometime after I went from zero military to three Defender-type ships, one in orbit around each of my planets. But the timing also correlates to my building a starbase halfway between me and the furthest AI so I could send a freighter. That wasn't in anyone's "territory", but I did choose to make it an influence starbase because that made more sense than military or economic for a range-extender base. It wasn't anywhere close to the AI that suspected me of something, however.
My best guess is that it's the sudden military buildup. The other two AIs that later on gave that message did so around the time I built up from those Defenders to military parity with some medium-hull ships.