I think you're experiencing the results of the new "flow control" features we added to the FAST platform in 0.31.
The FAST hardware does not do flow control, so we found that at times, MPF was sending data to the FAST controller quicker than it could process it, and we were filling up the buffer which led to dropped packets. (This was the root cause of what was causing some people to experience switch debounce settings not being applied to all switches.)
So what we do in 0.31 is keep track of how many commands we send and how many acknowledgement responses we get back to make sure we don't get too far ahead.
I searched your log for "flow" and found lots of entries like this:
2016-09-25 21:31:12,343 : DEBUG : FAST : Enabling Flow Control for RGB connection. Messages in flight: 4, Max setting: 3
So that's what's causing this here.
It looks like you have 158 LEDs? In my testing, I found that the FAST
controller could handle 128 LEDs at 50fps, and 256 at 30fps. So the first thing I would do is lower the update rate of your LEDs too. The default is 50 times per sec, but fast does hardware fades, so really 50 is probably overkill. Try lowering that to 40 or 30 or something. That setting is in the mpf: section of your config, called default_led_hw_update_hz:. Then search the debug log until you don't get those messages.
Also you can adjust the setting for the flow control to the RGB
processor by adding an rgb_buffer: setting to your fast: section. The
default is 3, so you can try increasing that which will let MPF send
more messages faster. You can try 4, 5, 6, etc.. until you don't see
those messages. If you want to disable this feature all together, just
enter some huge number like 100. (But in that case you'll probably drop some packets, which is probably what has been happening all along and you just never noticed.)
Now that they've identified this as an issue, FAST will increase their buffer and optimize the way they read from it in a future firmware release. In the meantime, playing with these two settings should get results that are good for you.