Set refresh_alt_ref_frame on keyframe encode.

On a keyframe alt ref and golden are refreshed.  The flag was
not being set and so on the frame after a keyframe, motion
search would occur on the alt ref frame.  This is not necessary
because the alt ref frame identical to the last frame in this
scenario.

Handle corner case where a forward alt-ref frame is put
directly after a keyframe.

Change-Id: I9be4cf290d694f8cf2f9a31852014b5ccf1504d3