The breakpoints located into the code of script that it is going to execute itself in a window aside from the main one are not captured by the editor or the debugger.

please specify in details what steps were performed and what script(s) were executed.
As far as I know breakpoints work fine

We call next javascript function when click on a special button located into the actual document form

function opensource () {
var oldtarget = document.forms[0].target;
var oldaction = document.forms[0].action;
document.forms[0].target = 'source2.php';
document.forms[0].action = 'source2.php';
document.forms[0].submit ();
document.forms[0].target = oldtarget;
document.forms[0].action = oldaction;
}

This function cause that a new window is opened. If I place a breakpoint into source2.php this is not captures by editor.

There is nothing strange.
You set breakpoints in the IDE. It keeps them locally until a debug session start. Read the posts below on how to get debug session started:
http://forum.nusphere.com/howto-run-debug-session-t585.html
and
http://forum.nusphere.com/how-to-debug-php-script-at-broswer-url-a-la-toolbar-t32.html