Point the flash at an even toned wall. Rather than using the sekonic flash meter in incidence mode, use it in reflectance mode held alongside the flash gun pointing at the same wall. This means both the auto-thyristor and the flash meter will be assuming an 18% reflectance exposure value from the same scene.

By using the meter as an incident meter you will be measuring the exact light output of the flash gun, however, if the scene infront of the auto-thyristor isn't 18%, then the flash will give either more or less light output until it does sense 18% reflected back, hence why the flash and the meter will give different results.