Nernst equation for a fuel cell when gases are stored separately
Given that the standard potential for a fuel cell is 1.229 V what is causing the difference in our measurement?

Multiple sources (e.g. here, here and there) estimate the voltage to be much less than the standard potential, especially when there is a load.

Individual fuel cells produce relatively small electrical potentials, about 0.7 volts, so cells are &quot;stacked&quot;, or placed in series, to create sufficient voltage to meet an application's requirements.

So it is surprising that the voltage is higher than the standard potential. Perhaps two cells were stacked to provide about 1.4 V, similar to the voltage of a standard alkaline battery, and about twice what you would expect from a single cell under load.

For [H2] I am using the molar concentration of the gas in its containing cylinder (I believe this accounts for water vapour).

For the standard hydrogen electrode, the standard state is defined as a partial pressure of 1 atm. This is much lower than a concentration of 1 M. In any case, the Nernst equation does not predict a voltage that is significantly higher than the standard potential.