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A major different between PHP 4.0.6 and PHP 4.1.0 is that 4.1.0 provides the "superglobals" $_GET, $_POST, ..., which can be used in place of $HTTP_GET_VARS, $_HTTP_POST_VARS, ...
The superglobals are not supported by PHP 4.0.6.
These variables are used to pass URL parameters, form fields, cookies, etc.
I just checked, and XOOPS 2.0.7 uses the superglobals in some places, so that would prevent it from working with PHP 4.0.6.