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.

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