Are you getting large values as per your title (which could be normal behaviour), or large delta values ( dX = X(t)-X(t-1) ) different from those you get with the cursor enabled and the same mouse movement?
With the cursor disabled the values are still in screen coordinates relative to the upper-left corner of the client area of the specified window, but unbounded so can be large.
However you should get the same delta for a given mouse movement as you get with the cursor enabled.
I would do a test with the latest code from Github if possible, and if the problem remains create a new issue on Github with as much information as possible. If you need help with creating the issue let me know.
For all the others Arch linux users that may end up here:
Through pacman I had installed the glfw-x11 version long ago. After some time and many updates it turns out that I now run on wayland.
So uninstalling it and installing glfw-wayland version fixed things.