Just a quick "Me too!" on this issue. I have also seen this, and have tried to reproduce it, but have thus far been unable to do so.
Yup - tooltips block button clicks here as well. Since you're likely layering the tooltips as objects over the window and the button, the OS is likely trapping clicks to them. I'm not sure how to best allow the clicks to pass through since I don't know how you have it set up.