A few friends and I have noticed the same thing for a while now - not just this last war. When they initially added the chests, it seemed like the success percentage on the 1st chest was 75% or more but it seems more like 50% now at best. Also, many of us are on Windows/Windows Phone so the app crash we often hit when getting to the chests (since last patch) lowers the effective percentage even more.
As others have mentioned, it would be great if they just made the 1st chest in war seasons a 100% success rate so there would be a guaranteed bonus if you take out the enemies gate. I had a particularly bad run of luck with chests (and crashes) in one of my wars yesterday and produced far fewer skulls than normal as a result which is frustrating.