Graphs1090 will check the message count every minute and calculates a rate from that.
graphs1090 looks at readsb stats … the message count tar1090 gets from readsb is a slightly different code path and includes stuff messages which are received for an unknown aircraft i believe while the number that goes to graphs1090 might not.
Never cared enough to clean up the inconsistency. (similar goes for ModeAC messages being included in the webinterface message rate but not in the graphs)