Same problem, but only since today.
Keeps on reoccuring every single time I attempt to start FL, no matter how often the problem is ignored, quarantined or deleted (apparently the freelancer.exe cannot be deleted or keeps being restored by something), the "always ignore" option does not seem to change anything either.
Also keeps on reoccuring after making a completely fresh Freelancer installation (which, on it's own when not having CF installed, does not have this problem), a completely fresh mod manager 1.31 download&installation and a completely fresh Crossfire download&installation (which took forever because 1.9 is huge).
Thus I doubt there is a problem with my Freelancer version or the mod manager.
Uninstalling my antivir and then downloading and installing a different one changed nothing, it was still detected every time and neither ignoring, nor quarantining or deleting did anything at all.
So it cannot be an immediate problem with avira antivir.
An interesting note: If I hammer the "play singleplayer" button fast enough (before the launcher can start downloading any files), it will display "Problem starting Multiplayer [E7]" (or E6 or E8 or so, it's hard to recreate and look which number, but it does say multiplayer for some reason even though I try to start singleplayer) instead.
So since it is the only thing that could potentially have changed anything about multiple people's FLCF files from yesterday to today is the launcher, it is The only suspect thing left, but if OP says he did not change anything about the .exe file there is no reason not to believe him.
Anyway, not that I'm accusing anyone of foul play or something, it's just that the game doesn't work while this problem persists. The usual ways of dealing with problems like this do not work.