1) Your sorting machine is backlogged as indicated by the red light at the output side, there's something there that has no destination. RP devices will NOT output into a tube if there's not a valid inventory somewhere to put it, when this happens things get backlogged and it all stops. If the sorting machine is backlogged, the filter no longer has a valid destination to send things. Place a chest over the tube at the sorting machine to see what's jamming it.
2) place the enderchest directly next to the sorting machine and put the sorting machine into self ticking mode (its the selection box at the top and it'll have a dot in the center with arrows flowing around it or something. The sorting machine itself will pull out of the chest in this mode (you won't need a timer or anything at all), you don't need the filter unless you're intentionally having it leave items in the chest. If that is the case, use the filter on the other side of the sorting machine and have it filter out black items and direct them where ever your trying to get them (your configured default coloring).
I hope that helps