Plugin Manager causes N++ Portable to lose settings

I just used the Plugin Manager to uninstall Light Explorer (which I previously installed), and now every time I start up Notepad++, it asks me to apply pending actions. When I do that, it goes through the motions, then restarts, except all my customizations have been lost. If I then close N++ and restart, the plugin manager asks to apply actions again.

Looking into this further, it appears that when the Plugin Manager restarts N++, the launcher thinks it's finished and cleans up. Then N++ starts again, but with default settings.