Fix two-pass framrate for Y4M input.
Fix two-pass framrate for Y4M input.

The timebase was being set to the value in the Y4M file on each
 pass, but only doubled to account for the altref placement on
 the first past.
This avoids reseting it on the second pass.

Change-Id: Ie342639bad1ffe9c2214fbbaaded72cfed835b42

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