Is there a way to flush the output of a PHP debugging session when the session is stopped (e.g. at a breakpoint), so that the output window would show the HTML generated so far?
Currently the output appears only at the end of the code run.

Output window (the one located on the bottom right corner by default), contains all the output generated so far. Do not mess with "Output" tab that contains embedded IE and won't show anything until it gets closing html tag.