I ran into a similar problem and came across this thread trying to track down the cause. In my situation, I found a Forefront Defs package a prior admin had setup that was pointed at the root of our package share \\<server>\Packages, where we are storing all our update packages. The package was also being updated by an automatic deployment rule.
My guess is the ADR was running, seeing folders that weren't part of the Defs package at the root, and clearing out everything else, like: \\<server>\Packages\Win_7_Updates, \\<server>\Packages\Win_8_Updates
I've pointed the Defs package to a subfolder, am rebuilding my other packages, and will see how it works out.