Hi Lemia -
I have the same camera, so hopefully I can help a bit.
First off, shouldn't your sequence preset be 1440x1080?
Secondly, if you have recognition problems make sure that:
a) You're only using one firewire port at a time. This camera get a little cranky if other things are plugged in.
b) Cycle the way you turn things on. For instance, you may have better luck if Final Cut is up and running before turning the camera on, or vice versa. I've noticed sometimes this makes a difference for me, sometimes not.
As far as capturing what you want, that may be a timecode issue. Do you pad in some time before and after you shoot? It may be trying to identify separate clips, and having trouble because there isn't much handle. What happens if you select the 'Capture Now' option instead of capturing using in and out points? Try getting a chunk in there and seeing what happens.