I had to boot into repair 3 times before it actually sorted out the booting requirements. I think users should note that when the setup screen says, after selecting Repair, that it may boot the system a few times that in fact it means YOU may have to make it so this.. It would be possible that the unwary would think the first failed attempt was indicating total failure. Never the less, this latest installation/repair interface beats the heck out of the older "Press F8" to continue, or go to the Command line to do Dos type repairs etc, for the uniniatiated.
It seems to me that on a dual boot sytem, partucularly 2 partitions on the one HDD, that the second installed OS is somehow dependant on the first.. I guess this is where the "system" flag comes in?
Anyway, all's well and I've learned alot.