If you have a system disk with multiple versions of RedHat Linux (e.g. a test version of Linux on hda4 and your "production" version of Linux on hda6), the RedHat 6.1 upgrade option only finds the first partition and performs the upgrade there. It doesn't find the second one and let you perform the upgrade on it. This makes it difficult to "test" an upgrade before doing the actual install.
This is fixed in the latest version of the installer available in RawHide.