I don't know if PSX games really used it, but the DualShock controller was capable of L3 and R3 (pressing the control sticks down that is). L3 and R3 would be the formerly unused bits in the first button byte. How about the buttons being sent active low?
Also, what would a controller that is not connected look like in the .pxm file? I assume it should be 0xFF since the DATA line is usually high.
/edit: According to protocol (which you're seeming to follow) the right control stick is sent before the left one. Also, the mouse information seems really weird.
http://www.gamesx.com/controldata/psxcont/psxcont.htm will provide you with more details.
I'm sorry to rant so much, but I've been fighting to get several controllers to communicate with a microcontroller and so I think the protocols should be followed in order to help others who might stumble across your documentation for reference.