This *may* have something to do with yesterday's ARMA3 update. Wilco had some difficulties getting Server #2 to update correctly, and it's possible he may have had to spoof the Steam Update system into thinking we were on the Development/Beta code-branch, in order to get the damn thing to download the files properly. It seems Steam was either inundated or overloaded yesterday, during the update period.
I don't believe that anything is likely to be different - as you quite rightly say, the Beta period is long gone, and the server-code is the same on the Beta channel as it is on the Stable channel (but I'm not sure about the Development channel though, it must be said).
You might also find that this only happens on Server #2 and not Server #1 (I remember Wilco saying something about them being different, or at least, Server #1's update happening without any issues.) Please let us know what you find.
I'll get him to have a look at this today if I can - (I'm currently 'in-hiding', trying desperately hard to get the new Altis Life 3.1.4 version from Tonic into some sort of 'parallel universe' with our own, branched-off server-code, in order to have the new features but with our own unique ALUK flavour.)