I've had the same problem recently with the AE-FF2 Airstream Protective Shell (2.5m).
I've tried with and without mods (I use a bunch), but with the same result. I first thought it was because I had such an enormous ship that it was overwhelming my PC or something, but it turns out that my standard lander (called Manley) was causing it, or rather, its AE-FF2 Airstream Protective Shell. When that shell is removed, the rocket loads and launches just fine. With it, it explodes. I've used this standard lander for quite a while, in fact on basically every mission, so this is a new problem with a tried and tested ship.
In the log that pops up when everything goes to hell, the first thing to happen is that the airstream protective shell (hereafter named AE-FF2) collides with the part above it, which in my case is a separator. I switched separators from the TR-XL Stack Separator to the Rockomax Brand Decoupler, and then something interesting happened. Instead of exploding, the vehicle (lander inside the closed AE-FF2) bounces way up on the launch pad, and falls down again. I'd say it goes a few dozen meters up or so.
It seems like the AE-FF2 is "jumping" somehow, causing an explosion under unknown circumstances but a thrust upward under some other.
The build ID from the config that the internet told me to report as the version is:
[config]
build id = 01804
2017.05.25 at 19:56:39 CEST
Branch: master
language = en-us
That date, 25th of May 2017 is probably around the time I started having this problem. Haven't really played since, because I was hoping that the problem would go away with something being updated.
That's all the information I have currently.