3 way light switch with timer - flickering
Thanks for the tips.

I had removed all the wires, taken pictures and was going to test the configuration again to double check that everything was correct. I was emptying the timer box and noticed a black wire there. I thought it was odd to see a wire there.. I re-read the instructions and it turns out I missed a step! As you can see below, there is a step "E" - After installing that wire the switches are working correctly.