I don't just mean the rules, though they're troubling in and of themselves, but there seems to have been some sort of internal shift as well. Trask for one looks about ready to have some sort of mental breakdown, to the point he's asking us what to do. That's not normal, is it? Team Leaders across the board appear to be having some sort of particularly odd reaction and I'm not entirely sure the constant training and new regime rules are what's got them off kilter. I'm not sure if it's that they know something or because they don't know something and are getting a little worried or angry or something in their own right because of it, but something's definitely shifted.
I don't even think it's VR necessarily, at least not by itself. The knowledge of the serum being kept and this new threat from them might have been a catalyst, but I don't think it's the whole story. If there are (and likely have been since the beginning) clandestine operations going on, they're usually more subtle about the ways in which they exert power. I'm not sure it's completely about testing. We've all used the same medical facilities, so it isn't as if they don't have materials to work with
The only thing I can come up with is that something behind the scenes, likely with the 'higher ups' has changed or they've found some new information they don't feel like sharing. There's just too much going on and too many variables and even I can't seem to find something that unifies everything into making sense.