There was an interesting discussion on wp-hackers about how best to store many-to-many relationships between posts.
The conclusion was that custom fields are probably the worst solution. While creating a custom table is the most straightforward way to do it, using a custom taxonomy has the most benefits. The most important one is that, when done right, no hand-written SQL is required.
So, this version of the plugin uses a hidden taxonomy to store the connections between posts.
If you were using an older version of the plugin, go to /wp-admin/?migrate_p2p to migrate your connections. You should probably make a database backup beforehand, just in case.
Besides that, the parameter order for p2p_get_connected() and p2p_list_connected() were changed. See all the API changes.