Help: What's the difference between functional simulation and timing one

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I added output pins to look at internal signals, but they don't usually show up when I run simulation.

I choose view, utilities, then nodes, list all, then select all, then close that box. This should include all inputs and outputs show up on the timing chart.

Which tool should I run next to make sure that the last pins I added will be included in simulation?

Oh, BTW, what does it mean when the timing chart shows hash marks superimposed onto the expected output wave form? No white space where there should be ones and zeroes.