I never install to partition - always use mbr. Message sounds like it will only install in partition below 1023 cylinder - so presumably you haven't got a 'free' partition slot there. I'd just use the mbr, unless you have a particular objection.
I've had CHS warnings like that before (also having created partitions 'correctly' - though if you use different methods for creating partitions on the same disk - eg, disk management & PM, I think you may get this) - there's never actually been a problem in use (and in fact, PM 'fixed' them - but can't remember what I did with PM to achieve this - might have just run it, and it found & fixed geometry discrepancy). Author says boot-us does a disk geometry check and displays warnings if it finds discrepancies (it will also display errors for more serious problems - I've had that after ghost created a 'virtual' partition on my machine where there wasn't room for one!). So I wouldn't worry about it - run PM & see if it fixes it?