I found in your code:

$phxVars = $_REQUEST;
if(file_exists("phx_config.php")) include("phx_config.php");
phx_reset();

but in phx_request() I found:

$_REQUEST[$qw[$i]] = isset($qw[$i + 1]) ? $qw[$i + 1] : "";

It means that after calling phx_reset() $_REQUEST contains more variables than $phxVars. It is bad idea. After that you wrote in documentation:

"This array contains variable values, initially it's copied from $_REQUEST, which contains all $_POST and $_GET variables and values. It's used to make your application modular. If your command file uses this array instead of $_REQUEST, then it can be safely called by the "phx_mod" function, meaning your command file can safely act as a module, which can be executed from within another command file and its output will embedded.

I can't use $phxVars because it doesn't contain variables I passed to the application with phx_url() function. They are added just in phx_reset().

In my opinion the code should be:

if(file_exists("phx_config.php")) include("phx_config.php");
phx_reset();
$phxVars = $_REQUEST;

Now $phxVars contains ALL variables.

Best regards,
Aleksander