Hm. This works for me fine since years. Had you check your global conversion template in preferences for format MOBI and AZW3 output options looks like? As BR wrote, the global template "defaults" will be overwritten from a manual changed template for a individual book. To reverse this behavior you need to set the preferences to default for these books.
A behavior that I really like because I don't need to think about original vs manipulated conversion behavior. My standard behavior is to manipulate as less as possible during a converting process and do modifications only if a default setup or a book design so poor that I need to correct to become it on a reader readable.
The only thing I am sometimes missing is a easy way to identify books with a non default individual conversion setups within the library. Maybe an enhancement for a plugin?
