Turns out, all buttons (even in the editor were beeping). I had not noticed it before because I don't always hit enter on dialogs. Turing off the system default beep sound removed the beeping.
Other windows apps did not cause the beep, just Lazarus and apps built with Lazarus, so the LCL must treat hitting the enter key and accelerator keys on buttons as default.
So not sure if that is the correct solution, but it worked.