The Xmegas are a great series of chips, but they still have some rough points...
The Errata notes that there are several NVM Controller instructions which are not operational, (Rev. H: 0x2B, 0x2E, 0x2F, and 0x3A).
Add the "Write Lock Bits", 0x08 command to the list, at least on the Xmega64A1.
Instead of writing the Lock Bits, Byte, correctly, it writes all 0's, maximally locking the chip.
The work around is to use the "Write Fuse" command for writing the Lock Bits. This command will write both the Fuses and the Lock Bits correctly.
Don't even ask how many HOURs and HOURs it took to sort this out... :evil:
Hopefully this will save someone else the same hassle.