Your normal alternator has no permanent magnets in it. It uses a copper coil for the magnet, meaning if there's no electricity to excite this (field) coil, you aren't going to get anything out of it because it isn't a magnet without at least a little power.
It's different in a PM alternator because there is always a magnetic field, so all it needs is rotation to start generating electricity. A permanent magnet motor will generate electricity the same way.
Edit: BTW, PM alternators are rare, so I doubt you've seen the insides of any with neodymium magnets. If there was copper wire in between the "magnets" then they weren't permanenet magnets at all. They were probably just iron-cores for the electromagnets.
[This message has been edited by Stubby79 (edited 11-22-2012).]