There is only 1 logical disk (RAID 1 configuration with 2 physical disks). When I say the "install was successful" I mean that the upgrade was successful according to the installer, i.e., it detected the existing installation, prompted for upgrade, etc., but in the end the server stays at ESXi 4.1. The installer was on a DVD - ESXi 5.5 ISO burnt on to it. As there is only 1 logical disk, it is both the boot disk as well as the content/data disk.
The only other thing I can think of that could be relevant (although I'm not sure how to get around it) - this R710 came pre-installed (Embedded) with ESXi 4.1 Trial from Dell. Maybe they created a separate partition???