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Is anyone having conrtoller issues with Ys IX, specifically with the D-pad (I'm using a Logitech Gamepad F310). When moving Adol with the D-pad, he always jerks to a complete stop after a few steps, especially when making circular movements. When the mode button is off (swapping D-pad control with the analog stick) the problem isn't there. However I prefer using the D-pad for movement so I find it rather annoying.

Note: My controller working properly, it doesn't have this problem in Ys 8.
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I have experienced the same. Seems to be whenever you try to go diagonally with down/left. For whatever reason that direction doesn't register.

And similarly, I had serious issues just getting my generic controller to work at all with this game. It didn't even read any inputs whatsoever before I put in x360ce, and even then I still have this issue you mentioned. Even Ys VIII at least registered my inputs natively without the need for x360ce.