Not entirely sure what happened, but now each time I launch Stencyl it asks me to accept the EULA and log in.
On the About, it's version is listed as "null (bnull)".
It won't save my editors for art and audio either, resetting them each time I launch.
I've uninstalled Stencyl, rebooted, and re-installed, then rebooted, but have the same problem.
EDIT: I noticed in the logs that it was looking for a "prefs" folder, which when I checked, wasn't there. I made the folder, and now Stencyl launches fine. But there are still other problems, like the version "null" thing, and trying to update tells me I'm not connected to the internet.