Question: Have you tried, with that new 128gb CF, plain-formatting it (builder_bigdisk_v21.upgrade), and then see if you get errors when you sync an album to it, i.e., without copying fids or the dynamic partition first?

That way, you rule out any potential problems that may have been induced with the copy operation with the PATA adapter that you performed on the linux box.

If that works, then you could try doing the copying inside the player, with the instructions here (scroll to Step 7: Copying files (special circumstances only)).