A manufacturing change in the new iPad (Check out our iPad review) appears to have broken compatibility with certain Smart Covers, as well as some third-party cases that use the iPad's built-in magnets. From video and photo evidence posted at Mark's Hangout, it appears that the new iPad now uses a polarity-sensitive sensor to wake the device from sleep upon opening the cover, meaning that the magnet must be correctly aligned — apparently early Smart Covers were initially made with the magnet in question facing either way. Opening the cover and reversing the panel fixes the issue, though obviously somewhat hinders the cover's visual appeal.
Newer Smart Covers don't exhibit the problem, suggesting that Apple has changed the design specification at some point — possibly last October, when the line got a color refresh. Reports on the Apple support forums say that the company will exchange defective covers for new ones at the Apple store, and third-party manufacturers including Targus and Maroo are also offering replacements.