Lines which are started with a hash ('#') outside php-blocks are not handled correctly. As they are not counted as lines during the compilation process the executable lines do not match to the source-code anymore. Thus leading to "breakpoint is set on a non-executable line" errors.

Especially when working with CLI-script this behaviour is very frustrating as all scripts starting with a shebang-line (e.g. #!/usr/bin/php5-cli) cannot nicely be debugged. Because of the breakpoint-line mismatch the script will not halt on correctly set breakpoints.

Any hints how to resolve this issue?

This issue is a well known issue in php itself.
During long time php is fighting with shebang lines. In some version line numbers are counted well, in some they aren't.
Try to run the following code to check:



and make sure that the error says non_existing_function call is on the 3rd line, not on the 2nd or 4th.
In latter two cases, feel free to submit bug reports at bugs.php.net

As I know php 5.2.8 counts well. 5.2.9 does not.