Any plugin that emulates the noise produced by analogue hardware is quite likely not to produce the same noise twice in a row. It might, but since the noise component is basically white noise and fake hum it might not.
On the subject of noise, if any plugin is creating noise, e.g. a synth patch, then that may well not be the same twice. Not if it’s properly randomised anyway. Reverbs might not produce identical output on every run through a track either.
What might be worth a try, and I think eliminates everything but the audio engine, is to load a stereo track, commercial or one of your own into a fresh project in each Sonar version. Use no plugins, not even eq and no dithering. Then bounce out from the Master bus at the same bit depth and sample rate as the project.
Do this twice from each version. If S5 copy one nulls S5 copy two, and the S6 renderings null each other, then that shows both versions are rendering the same thing, or as close to it as matters, every time. Then try nulling a rendered track from S5 with one from S6 and see what happens then.