Two major fighting game communities, as well as a few of our readers, are reporting problems with a certain third party joystick and the new slim PS2 unit.
Specifically, some models of the Pelican Real Arcade Joystick for PS2/Xbox/GameCube do not seem to work when connected to the latest model PS2. So far, neither Pelican or Sony have released a statement.
This problem appears limited to Pelican's multi-console Real Arcade stick, and doesn't seem to be the case with the company's line of single-console Real Arcade sticks (e.g. sticks that only work with one system, such as the PS2).