If the last note was deleted with Ctrl+Q (or Menu / Delete), then a new blank note window appears that can moved, but removes itself immediately back to the screen center. If re-appears immediately after closing it, too. One can just kill the plugin and restart it.
Version is 1.6.4, default options in ./configure, build on Slackware
Fixed in svn r6859
Btw, for a temporary solution build with --disable-fs-monitor