My only experience with Schengen visas has been watching several of my Thai friends apply for, and use, such visas for EU (Schengen states) travel. To my knowledge, they've applied to the embassy/consulate of the country of their first entrance to the Schengen territory, and then traveled freely without difficulty. I know the French are sticky in their rules about max time in country, but I would be surprised if they were even able to ascertain the time spent in other countries, given the general lack of entry/exit stamps applied at immigration checkpoints.