I am fronting the startups fees for my cofounder. Will this be problematic with VCs and Angels down the road, or is it common?

No.

I did this. I funded our beta myself. No one cared.

Generally, VCs will be fine if it really matters if the company reimburses you for incorporation and other trivial costs from VC proceeds. If this number becomes much more than a few tens of thousands of dollars, though, it will raise a flag.