No speed hacks are used and on default cycle rate.
Advanced setup is on default.
I've attached the main config screen so you see all the plugins.
Tried this exact setup on Pcsx2 0.9.6 and 1329 Beta.

So no one has any idea what could be wrong with my setup?

Edit: Ignore this, I read wrong

You could always try a newer rev of lilypad I have the same pad and never had any troubles with it. Well besides pad related troubles that some of the buttons stick sometimes.

That was what I mentioned in my now edited post, but he already has the latest public beta revision, and as far as I know there is no newer... Or am I wrong?

well according the screenshot he has r1034 which is pretty old on my own compiles I have r1388

There is no newer unless he want's to compile the game himself.