FCP must be set to access Ch. 3 & 4.
Here’s how (it is the same for PAL, but you will of course use the PAL settings):
Final Cut Pro (menu pull-down) >
Audio/Video Settings >
Capture Presets >
Click the “Duplicate…” button >
a new “Capture Preset Editor” window will open >
Change the “Name:” field to DV NTSC 48 kHz CH 3&4 (so you’ll be able to tell it apart from the “normal” setting.)
Under QuickTime Audio Settings >
Input: Second 2 Channels >
Click “OK”
Now, try a capture. If the audio is on CH 3&4, you’ll get it into FCP.
Remember to put your “normal” settings back (to “First 2 Channels”) after you captured CH 3&4 tracks.