In regards to the misplaced water, I'll look into it. Could you tell me exactly which level this is, so I can test any fixes on a level where the issue is known to occur?
On the other hand, in regards to the window position, they're definitely in the same spot as far as the image goes. Do keep in mind that NeoLemmix is not Cheapo and doesn't aim to perfectly replicate it; there are some features specifically added to improve compatibility (ie: implementation of all Cheapo object types except gravity changers (although some don't function exactly the same way), and the "Cheapo Mode" option), but at the end of the day, there will always be levels that need some manual touching up. This level may just be one of those.