For OS tracking to work correctly, both operating systems of the dual-boot nodes must have identical host names. Moab host names are case sensitive (even though DNS is not). You don't need to have all the host names capitalized on each machine. You only need to capitalize them in the TORQUE nodes file (/var/spool/torque/server_priv/nodes by default) for them to be reported in caps. You can change the case of node names in the MSMHPC Manager. Also, if SSH is enabled on both operating systems, the SSH keys should be identical to avoid SSH errors.
To make the SSH keys identical, boot all of the nodes into one operating system. Copy all SSH keys from the nodes onto the head node. (You can usually find keys in /etc/ssh and usually named ssh_host_*.) Then reboot the nodes and copy the keys to the other operating system. You may need to edit /etc/ssh/sshd_config to point to the new key files. Also, make sure the hostnames and IP addresses are identical.