Welcome to the forum.
Can't help but think it's either a poorly-sloped drain line from the toilet (you routed it out with a rotating plumber's tape, yes, when you replaced the wax ring?), or a faulty toilet. With today's low-flow toilets, it doesn't take much to plug a line. I'd be tempted to run a high-pressure flow of water in the toilet's drain in the floor the next time I took the toilet off, sealing up the opening around a water hose with packed rags. You didn't say the brand, model or age of the toilet, but if it needs replacing, you might want to consider a Champion 4 by American Standard. They have one of the largest trap openings on the market, and all of the ones I've specified (as an ADA remodel consultant) or installed have performed flawlessly.
Maybe someone with a stronger plumbing background will chime in shortly.