I seriously doubt a small intake leak or any tune parameters are going to trigger the service brake message. Fixing an intake leak will make it run better though. It will lope a little more with a bigger cam, so maybe that is what you are feeling,
@Geotrash could confirm or dispel this last idea though. Also, with tuning, it is all about the skill of the guy filling in the boxes.
There were a few threads a while back on the service brake message, one turned out to be a simple low fluid level, but the other had something to do with a bad O-Ring in the vacuum booster assembly. My search skills are poor, but you might try finding that one.
I think one thing you might try to help in diagnosing the issue is not think about the cam swap when you are thinking about the brake issue. It likely is just a coincidence it happened shortly after the cam swap. It could be related, but the odds are a lot greater it is something else.