correct alt-ref contribution to frame rate

When producing an invisible ARF, the time stamp counters aren't
updated since the last time stamp is seen by the codec twice. The
prior code was trapping this case with refresh_alt_ref, but this isn't
correct for other uses of the ARF. Instead, use the show_frame flag.

Change-Id: If67fff7c6c66a3606698e34e2fb5731f56b4a223