Last night I got an update message for a new 2.6.20-14-generic kernel so
I figured what the heck, I'll give it a try. I downloaded and installed
the update and what do you know the thing actually boots without any
problems. I'm a little confused though because I'm not sure if they
released the 2.6.20-14-generic as a newer update to the old
2.6.20-14-generic and just didn't change the version number or what.

Something I did notice though, some of my hdparm optimizations like
multicount and such no longer initialize in this drive using the new
libata driver. My read speed went from around 60mb/sec down to 28mb/sec.
I'm guessing this is still early code and over time will mature more.

One thing of note, on my system I had to disable most of the ide tweaks
in the bios just to get the thing to boot with the 2.6.20 series
kernels. I should add that I have two internal drives, one a 20gb and
the other a 400gb. Ubuntu is on the 20gb and even with the older 2.6.20
kernels would boot okay, so long as I disabled things like UDMA access
and DMA transfers and stuff in the bios. The 400gb drive is the one that
gave me all of the problems regarding the host protected area and is
what lead me to this thread. I have not tried enabling most of these
tweaks in the bios with this "new 2.6.20-14-generic" kernel that
recognizes the 400gb drive correctly. I will have to try that tonight.

-- 
pata driver in libata is thwarted by HPA
https://bugs.launchpad.net/bugs/82314
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