Violation of the I2C bus protocol. A slave must be able to stall the master when it needs more time for processing the access. This is called "clock stretching". If the GPIB card stops the counter from working I'd just remove it. It doesn't work anyway so it doesn't make any sense to have it.
Thinkfat, therefore I think that this will place a nice nail in the coffin. I am wasting too much of the precious time of all EEVB members, and I am extremely grateful for all your help, at this point I will just remove the GPIB card for good and close the meter.
Maybe I'll use the option connector on the M/B as convenient way to power a OCXO inside the unit, simply routing the output externally using a 4cm BNC patch cable, the meter will see it as a External ref, and that's it.
But it has been a great ride, and I have learned a lot!
Just for info, I will remove the CPU once I get back home and see what the clock looks like without it... All my best, Franco