Just to be sure: You are not looking at the BMR of the day where you did you last synchronization between watch and GC, are you?
BMR is accumulated over the day, and when you synchronize, you get the accumulated BMR for the time of synchronisation. So if your daily BMR is 2400, and you synchronize at noon, you will only see a BMR of 1200 in GC for that day. If you do a new synchronization the next day, the value will be updated to the BMR for the full day.