Well, it has taken a while but I think I have finally tracked down all my clipping issues, it has been a real struggle because it turned out I had several different sources of clipping. They were:

• Very, very obvious and nasty clipping on my main test track (Don't Panic from the Coldplay album) from the very start of the track. This only effected my Mk2a and looks like it was due to the corrupted eq settings as I documented earlier.
  
• Subtle, but irritating clipping throughout my main test track. It turns out that my CD-ROM in my main desktop machine has a secret dislike for the Coldplay album, resulting in small amount of clipping when ripping it. The CDROM in my server doesn't have this problem and even though AudioGrabber was generating the same checksums using the two different drives there were differences in the WAV files.
  
• Even more subtle clipping from 36 seconds into the track, to the end. This one took a while to track down (though it was clear early on it was nothing to do with my empegs). Somehow a little known feature (to me) on my SoundBlaster AWE64 had got turned on. The feature is called "3D Stereo Enhancement" and it would appear with some tracks, including my test track, it can cause subtle clipping of the output...
  

So I have had a fun couple of days...