My guess would be (since the Tundra has very soft paint) is that you're inducing some micro-marring that you're not fully taking out.
My suggestion would be to hit it with a soft polish pad and the lightest polish you have at high speed on the Flex. Work on small areas, moving relatively slowly, and give it several passes per area. Keep the idea in your mind that you are trying to burnish/jewel the surface.
I've got a lot of pinstriping, marring, and webbing on my truck right now from a full season of taking it through the woods, and I am doing some testing areas (and touching up small rock ships) for polishing, and I can remove almost all the marring with Meg's Swirl X, which appears to be a relatively mild polish. Some of the heavier marring looks to need something heavier, and I have in mind to try the newest Meg's Scratch X which is supposedly a comparable step to Meg's 205 (it's in-between Ultimate Compound and SwirlX, at least by my research).
TL;DR: Tundra has soft paint, and you should be able to get it mar-free using pretty light polish and a polish pad with the Flex.