Thank you for all of the replies, gents.

The shop pulled out the antenna cable and gave it a thorough inspection.  They weren't happy with the connectors, which appeared to have been attached with an incorrect crimping tool, and the length of the cable (too long). 

They shortened the cable (it is RG400 from what I understand) and affixed 2 new connectors.  It appears to have solved the problem, the GPS reception was rock solid on the 1hr flight that followed.

The working theory is that the antenna cable was somewhat dodgy.  The interference caused by the presence of some piece of hardware associated with the canopy was enough to degrade the signal to the point of failure.

I had ruled out com radio interference by testing the system with the other com radio completely switched off.

So far, so good!

Keith