IIRC tooltips are separate windows just like popup menus, and although I'm only familiar with the X11 side of things, I'm thinking there's a window attribute flag FLTK isn't setting for tooltips that needs to be set so the window manager doesn't keep moving focus around. I'm not sure what that is, and did try to look into it once by looking at other toolkits, but couldn't quite figure it out.

I can confirm the OP's behavior even on Windows 7 with my own commercial app.. I never noticed it. I don't have a patch or know what to fix in this case.. win32 is not my specialty at all.

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