Fixed bugs in multi-layer code related to changing params

When running multi-layer (ML) encodes and dynamically
changing coding parameters on the fly (e.g. frame
duration/rate, bandwidths allocated to each layer)
the encoder would not produce sensible output.

In certain cases the rate targeting would be
hideously inaccurate.

These fixes make it possible to change these coding
parameters correctly and to maintain accurate control
of the rate targeting.

I also added the specification of the input timebase
into the test program, vp8_scalable_patterns.c.

Patch 2: Moved declaration to appease MS compiler)

Change-Id: Ic8bb5a16daa924bb64974e740696e040d07ae363