I've got a similar problem with my mum's dapper installation.

I installed the current 2.6.20-generic kernel from the feisty respository on a 
dapper machine,
to fix a problem with not detecting a USB scanner at power-up (needed to 
unplug/replug to see it)

However I found in about 1 in 5 boots the 2.6.20 kernel failed to boot,
with it waiting for ages with:

Begin: Waiting for root file system... ...

whenever this occurred it was preceeded by a:

hda: ERROR PORTS ALREADY IN USE

Its seems it might be a race condition, where the via v82cxxx driver
doesn't always claim /dev/hda before ide-generic does. Which causes the boot to 
fail.

After a while in the fault contidition it drops into a busybox shell and 
I found only/dev/hdc the cdrom drive was listed in /dev

Not sure If I found a fix, but its booted 10 times without problem since I 
commented the ide-generic and recreated the 
initrd file for the 2.6.20 kernel as sort of explained in bug report 76872

-- 
ide-generic: load conflicts with IDE drivers (PORTS ALREADY IN USE)
https://bugs.launchpad.net/bugs/26998
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