I may have misread your problem... if it is indeed the trunnions misaligned, this is a much more serious problem. And since the saw is this new, and HF does have a good return policy, then it may be prudent to exchange it..........
I was thinking it was just blade alignment, which , I think, there are some relatively easy fixes.
Here is the method I use to determine my blades alignment, -- of course the little strip of metal can be longer to get different readings. (And, yes, that isnt a HF saw, I got one of the 'swivels' ---- after I wore the HF one out)
If everything seems to be going well, you have obviously overlooked something........