kof94te is at version 1.3.0, out of beta, including the patch for this problem. By the way he could confirm the problem happens only on raine, not on the original hardware, so maybe 1 day I'll have to change the way sprites are drawn. But for now it allows me to do things faster for sure, so everything is good.
I can keep the patch in the source since it checks the contents of the rom before patching it, so it doesn't try to patch 1.3.0, just tested with the a95 patch.
This is the end of this problem then !