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This situation happens whenever you put on include path other netbeans php project. Every breakpoint from other project will be skipped and not send to xdebug and then naturally xdebug won't stop execution on them.
http://hg.netbeans.org/main/rev/eb59cd174c2f
verified on Windows XP Pro SP3, jdk1.6.0_06, XAMPP 1.6.5 (PHP 5.2.5 XDebug 2.0.3)
Integrated into 'main-golden', will be available in build *200902270313* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/eb59cd174c2f User: Radek Matous <rmatous@netbeans.org> Log: #159141 skipped breakpoints from files on incl.path && from other projects