I have Sam and Max the Penal Zone on an iPad 2 with iOS 5.x. when starting a new game everything runs fine. But after loading a saved game (or switching between apps) the virtual joystick to move Sam disappears and Sam cannot be moved.
FYI - this used to work with iOS 4.x installed, but has never worked for me on any of the iOS 5 upgrades.
p.s. the new (season 2) Sam and Max games are running great!