My workaround is this:
Move "Installed Packages", "Packages", and my license file out of the data folder.
Delete the data folder.
Reopen Sublime, and quit without even putting in my license.
Delete the autogenerated "Installed Packages" and "Packages" folders.
Move the old "Installed Packages" and "Packages" back, along with the license.
Good to go.
@jps: obviously this isn't a problem with my packages, because I just move the old ones back in. Deleting all the contents of the data folder doesn't work; I actually have to delete the folder itself. Let me know if I can give you any other info, because I'd love to see a fix!