It sounds to me like there may be a minor issue with the liner on the clip side near the pivot area. It could be that the liner is ever so slightly bowed/bent near the pivot and that is causing undue pressure making it hard to open when the screws and clip are absent, but when the clip screws engage the liner and hold the clip in place, that causes the liner to flex enough to relieve the pressure and make opening the knife smooth again. Just my theory.
As I see it, I don't think the issue is a big one at all and it can be remedied. Two immediate choices present themselves. Send it back to Spyderco and have them replace/fix it under warranty. Simple, fairly quick and almost painless. The other option is to add a drop of mineral oil to the pivot and work the blade back and forth and see if it "breaks in" after a few hundred openings and closings. Just play with the knife a little while you're watching a game or something. That is all it may actually need. You could go with option 1 if that does not work.
What I would NOT do is take anything apart and try to remedy it yourself as doing so would void the warranty. It's not that it's overly complex, but given that it's brand new and came that way, the warranty option is just too easy to do.