Just backed up my theory a little bit.

I dumped swapon -s into a file near the end of checkroot.sh and
confirmed that there was only one swap entry (/dev/sda9) at this time.
When the system was fully up and running, there were the two entrys with
and without 'mapper' again.

-- 
2 swap partitions each mounted twice in 2.6.20-8
https://bugs.launchpad.net/bugs/86234
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