It is telling you that it did not find any boot partition. Not that it is confused by your hard disk, but that it somehow can't find the partitions on your install CD.
Maybe the CD was not burned correctly, so the few first sectors work ok (enough to get the boot loader running), but somewhere later in the filesystem there is a problem. Maybe your CD drive has trouble reading it for whatever reason. Or maybe our driver for CD drives is incompatible with something.
So, wiping the hard disk is unlikely to change anything.
As for this not getting enough testing, in my case the problem is not "pkgman update" (I do that from time to time, but still). The main problem is most of my machines don't even have a CD drive anymore, and I do clean install from USB sticks as it is much more convenient for me. But I know we have some users keeping an eye on CD installs.