2009, if your son is moving into an 11+ senior school, he should be fine with the transition. The schools will be set up for entry from primary schools as well as preps.
I think that Floss' DS must be in a prep school that goes up to 13+ if he is doing the CE course. Basically, there, they either ignore the KS2/KS3 division, or finish up the KS2 course by Christmas of Y6 (if they have girls doing the 11+). They also finish the KS3 course by the end of Y8.
I would say that the school should really have covered any gaps early in Y7. My DS1 joined his prep school in Y7 and spent the first half-term catching up and then he was fine. He didn't do Latin, so used that time for the catch-up lessons.
Typically the areas where primary school children can be behind is in French, Latin if offered, practical Science, Art, Music, Drama, and Games (basically the subjects where prep schools have specialist teaching). It really shouldn't take long to catch up though, and the school should give the appropriate help (that is what you are paying for).