The plugin doesn't matter. I can re-produce it with every plugin that supports the help button/which has got an help button. To be explicit I re-produced it with this plugins: - Auto-Close - Auto-Mark - Code Navigation - Commander - Define formatter - GeanyCtags - Latex - Macros - Project Organizer - Spell Check - Workbench
I think it is not plugin related. The Number bookmarks crashed by just enabling/disabling it but that is definitely another plugin specific issue.
I will re-test now and see if waiting some seconds after the on-off phase makes a difference.