HI,guys:
The issue has been resolved. I found a document for the Fluke PM6690. The key to this problem was that my OCXO, pin 2, Vref could not output voltage.
However, during calibration, or when the OCXO is operating normally, Vref must output a 5V voltage. (Page 85 of the document)
I added a variable resistor between pins 3, 2, and 5 of the OCXO to allow Vref to output a 5V voltage.
When it can output 5V, I was able to correctly calibrate the time base.