Welcome to the forum @toromand
>Also, the X direction cuts much easier then Y direction
>It does not have anything to do with the orientation of the wood, as I have tried to rotate the same peace of plywood 90 deg and repeat.
My experience has clearly shown that the direction of the grain is absolutely critical to what speeds you are using to cut or surface burn a line or circle, etc. While you may have another issue with your Y axis, once you solve it, you will find if you try to cut a square for example using the same speeds for X and Y, when you are done and look at the back of the wood, you will see two lines have cut through and two lines have not.
The assumption is that you are making just enough passes to make the cut and not making extra, time wasting passes just to get through the two cuts that require more passes.
That's exactly why I designed BenCutLaser (BCL) to allow you to set an X speed and an Y speed. The results is that you can cut a square or a circle in 6 passes and when you turn over the wood, you'll see 4 very evenly cut lines or a circle cut all the way through, evenly.
On large parts, this is a really big time saver.
Anyway, that's been my experience.