A mouse event with so large numbers is discarded by Enigma on purpose, because the black ball would suddenly be subjected to an enormous impulse, if the mouse event would have been interpreted the normal way. So, the ball not moving is a logical and necessary consequence to an overly large mouse xrel/yrel-pairing. So ... we have to ask: Why does SDL2 report so large xrel/yrel-values?
I cannot reproduce the bug ... could you please answer the following questions?
Do you use a special kind of mouse or mouse port?
Do you use an intermediary program (like a logger) or a remote desktop? (Those might manipulate the mouse coordinates. The fact that you observe the same problem using VirtualBox can be explained by (1) VirtualBox manipulating the mouse coordinates or (2) the host OS being involved in the bug.)
Were there other windows on the screen, besides Enigma's window?
There is a bug report about SDL 2 here concerning "jumpy" relative mouse motion:
It needs other windows other than Enigma to be present. It should be closed on X11, but your host OS might still be reporting wrong numbers. However, the numbers you report are so much larger, that it just doesn't make sense, unless you use something like a 40.000 x 20.000 pixel display?