The keyboard shortuct used to flag/unflag a message in Mail is Command-Shift-L. This is the same keyboard shortcut StickyBrain uses for the Lookup Password shortcut. To solve this problem you'll need to change the Lookup Password shortcut in StickyBrain.

1. Launch StickyBrain.

2. Choose StickyBrain > Preferences, and click the Shortcuts button.

3. Change the Lookup Password shortcut to use a different hot key.