When I HPA'ed one of my HDDs, the partitioner, at least the Ubuntu partitioner, still showed the native size!
This was despite I know that the HPA'ing was successful.
This problem don't occur with Windows.
This can have bad consequences, just like when the HDD is hooked to an early PC, can cause sector errors, because of the OS attempting to access LBAs beyond the max that is seen by the BIOS.