Also, check to make sure that your spindle is square and true to the workpiece. Mine was off by a few degrees in both axes and it led to similar problems to what you're having. Get a carpenter's square (you'll need a small one, a 6" speed square is what I used). There are several other threads that have different methods for doing this, and I'm not saying mine is better or worse, I'm just saying how I did it.
I took all my measurements from the spindle mount itself, and took back-up or confirmation measurements off of the axis rails and the gantry extrusion. My figuring was that no matter what else is going on, if the spindle is what needs to be true, that's what I should measure.
Use the left side of the spindle mount as a reference point. It's the side that has the three extra holes drilled into it. Put your square flat on the wasteboard and push the spindle up to it. if it's not flat, you'll need to undo the 4 button head screws that hold the Z axis rail onto the gantry extrusion. Using a ball-end allen wrench, Undo three of them pretty loosely, only undo the 4th one a quarter turn. This will keep the whole rail from falling off in your hand. Now adjust the axis until the spindle mount is flush with the square. Then tighten the screws again. Now push the spindle away and re-check to make sure you didn't move it while tightening the screws.
Setting up square front-to-back is a little more tricky.
Again use the left side of the spindle mount as a reference point, except this time align the square perpendicular to yourself, against the accessory nub on the mount.
Using a T20 torx driver, pull out the screws holding the X axis to the endplates, and drill each endplate hole bigger. This will give you the slop you need to square the machine. Again, don't tighten the screws too much until you make sure that you're square.
Once you're square front to back, tighten all 8 screws, then make sure the gantry still slides back and forth easily and that the v wheels aren't binding up anywhere. Then check square again front to back and left to right.
You should notice that the bottoms of your pockets are cutting more smoothly too, and that in wood there's less bit-chatter going through denser sections.