AOPA's Flight Training magazine this month has an article that addresses issues like this! The "Legal Briefing" column is talks about interpretation of regulations by the FAA and their use in judgements by the NTSB in an accident or incident investigation. You should be able to see the article if you go to http://www.aopa.org
where they archive all the issues.
The thrust of the article is that there is a law on the books stating that the NTSB must accept as law any interpretation made by the FAA of a regulation as law. These interpretations are in the form of guidance published in the AIM, advisory circulars etc. So, if the AIM says it, you better do it! You might get away with flying with a faulty altimeter, but if you get into an accident they'll wipe your nose with it!