Over the past 10 or so years, Intel has been working with the BIOS vendors to move away from CMOS parameter storage. CMOS parameter storage is unreliable; it is actually possible for CMOS to be corrupted, purposefully or inadvertently, from runtime environments (I once saw this happen (I will presume inadvertently) during a Windows Sound driver crash and blue screen). For the most part, the use of CMOS has been eliminated in modern BIOSs. It appears, however, that there are still a few places in the BIOS code where CMOS is still being accessed (the proof is in the fact that clearing CMOS does make a difference in some cases).
JFFulcrum is correct. The one way to absolutely ensure that the BIOS configuration is completely reset is to reinstall the latest BIOS using the iFlash command with the "/f" flag on the command line. This forces the defaults to be installed as part of the BIOS update process. To do this, you must boot to DOS (MSDOS, PCDOS, FREEDOS, etc.) using a flash stick or something similar, however.
You mentioned that the hang occurred while attempting to use F9 in BIOS Maintenance Mode (i.e, with BIOS jumper in the 2-3 position). Have you tried using F9 in normal BIOS Setup (i.e using F2 during normal boot)?