It sounds like you increased the leverage against your gantry beam when you increased the height, This design https://openbuildspartstore.com/open...-beam-machine/ was minimal to start with, barely rigid enough to cut soft materials. No, it's not normal for gantry beams to twist visibly, but it does happen, especially when design parameters are exceeded. You can try replacing it with a stouter piece of extrusion, but that might just make another part of that machine the weakest link.