Biscuit joints vs dowels for face frames, I'm done with dowels and here's why
I built face frames both ways on the same kitchen job last fall, 14 doors total, and the biscuit frames came out dead flat while the dowel ones had two stiles that shifted a hair overnight. The biscuits give you that little bit of wiggle time to line everything up before the glue grabs, dowels lock in the second they seat and you fight them. I use a #20 biscuit with Titebond II and clamp for 30 minutes, no creep, no gaps at the joints after sanding. Dowels are cheaper per unit but the time I lose re-cutting a misaligned stile eats that savings fast. Maybe I'm just not good enough with a dowel jig, so if you've got a system that keeps them lined up tell me what you're doing, because I want to be wrong about this.
The variable you never hear talked about is humidity. Biscuits swell from the moisture in the glue and actually tighten the joint over the next day, while dowels stay the same size and depend completely on a good fit from the start. If your shop swings in temp and humidity overnight like most garages do, that alone can explain the dowel stiles moving on you. Fluted dowels are supposed to help by giving glue somewhere to go, but they don't fix a bore that was drilled a hair off square. Have you checked whether the shift was really at the joint or if the whole stile cupped?