I have been having this issue, but maybe it's unrelated. Right now when I don't suspend my VMware windows instance before closing the lid the battery will drain overnight. I was hoping this might correct that but no luck.
I'm fairly certain the VMware is your issue. My wife's rMBP does that when she leaves her Windows 7 instance running after shutting the lid. My guess is that VMware isn't allowing your laptop to properly sleep. Luckily for me, my wife has become less and less dependent upon Windows 7, so I don't get as many complaints about "dead battery" from her anymore.
I have a MbA mid 2013 and I did that update but before to do it, It had between 9-12h of battery life and now, MbA has 7 hours or less. I have the same software, I didn't install anything, I don't know what is the problem.
Ive had the odd battery drain for no apparent reason when the lid has been closed and it should be in sleep. The system also felt hot to the touch even though it should have been in sleep.
Nothing running in the background whatsoever.