Interesting... I am not aware of any limitation regarding parallel port vs. USB, but I haven't done any PHP development that required printing.
The question is... is the comparison being done on the same machine? If we're talking about two different servers, then there could be other factors. If I'm not mistaken, you have to enable the php_printer.dll in php.ini, and it only works on Windows machines. So, if you're on a Linux box, you might be out of luck.
Be sure to read the user comments at the bottom of that page. They might have some useful information as well.
One last possibility I can think of may be to use a USB-parallel converter, and use the printer with the parallel port. At the very least, if you get one of these converters, you can test the theory about parallel printing working and not USB.
Good Luck!