This is a common error in the ESTK (Extendscript Toolkit), I believe it's a bug - breakpoints should not get disabled by starting the script.
Most likely pressing F11 (step into) will also make the breakpoints turn into a darker red colour (disabled). But in this state (stepping through the code) you can enable the breakpoints again and they will get hit when you let the script run on (F5).
(Shortcuts are for the Windows version.)
Another thing to try is to first start the script from the scripts panel in InDesign (run it once), and then start it from the ESTK. If you use the targetengine directive to set a specific engine name, this might even be necessary.