This happens to me routinely. I asked why, but did not get replies yet. I moved my own packages out of ~/.julia/v0.6 so that I can wipe and reinstall it every month or so, and I am in the process of figuring out how to run tests for them.
“Running Pkg.update() routinely” turned out to provide the illusion of being up to date. Some packages were 2-3 (!) minor versions behind.