If you go over the Napoleon Pass, right at the top - some 5,000 feet, there is a small timber guard post where the customs officials wear traditional Napoleonic era uniforms (some hangover of tradition I suppose), and you have to trade in your French Euros for Spanish Euros ..
The day that we crossed the Pyrenees from Saint-Jean-Pied-de-Port the weather was very poor with freezing rain at the top so we took the van ride with the backpacks that other braver pilgrims didn't want to carry. At the point where we crossed over into Spain the van was stopped by the Guardia Civil,
one of whom was carrying a machine gun. They were very polite and checked everyones passports or European Identity cards, I had a feeling there might be a problem when I gave them my passport because when I flew into Paris from Canada it wasn't stamped at the airport. I was right they gathered into a huddle with my passport some distance from the van and after a few minutes sent one of the younger guards who spoke very good English over to talk to me. After I explained that I entered Europe at Paris and my passport wasn't stamped and that the year before I had flown into Rome and had the same experience there he smiled, returned my passport and waved us on.
Might have been around a time that ETA was acting up. The last time I was there (Sept 2007), the authorities had luckily foiled a car bomb plot in Logrono just days before I got there. There was still police tape up the morning I walked out of Logrono & there were wanted posters up in every albergue.