I don't know if it'll solve the problem, did you try to ''regenerate output products" and then re-compile and re-synth your design?
btw- Critical Warnings shouldn't be ignored.
I am almost sure this problem is entirely due to porting from 2015.4 to 2016.3.
Can understand your situation. Me too switched to Viv 2016.3 from 2015.4 this week and faced a some signal value display problem in the waveform viewer. My thread is still not solved under the sub-forum, Simulation and Verification --> Signal value not completely displayed in waveform window. Someone says that my problem is reported to the factory, don't know hen this'll be resolved.