autotest: drain mav before checking EKF values

May be getting stale values from this function

Tools/autotest/common.py

@@ -3376,6 +3376,7 @@ class AutoTest(ABC):
 
     def wait_ekf_flags(self, required_value, error_bits, timeout=30):
         self.progress("Waiting for EKF value %u" % required_value)
+        self.drain_mav_unparsed()
         last_print_time = 0
         tstart = self.get_sim_time()
         while timeout is None or self.get_sim_time_cached() < tstart + timeout: