Hi Jeff,
Yes, there is a significantly newer version of DPOJET available.
DPOJET is updated together with the firmware of the machine. Here is the latest version of the firmware (and DPOJET):
https://www.tek.com/en/support/software/firmware/firmware-dpo7000-dpo-dsa70000-dpo-dsa70000b-c-mso70000-c-doc-win-xp
On measuring relative jitter between two clock source's, that is possible by selecting a measurement like TIE, RJ or DJ, then going into "Configure", "Clock Recovery" and setting the Method to "Explicit clock - Edge" and selecting the desired clock channel.