Minecraft-pi offset two windows

Raspberry Pi gave me a strange behavior yesterday, as I tried to setup for my son to play minecraft (granted, I tried also to play the thing).

I installed raspbmc with retropie in my raspberry pi SD card, which works almost fine, only stella crashes too often… and snes is not that easy to setup to play, but I will get to this later.

I exited xmbc, typed startx, and could not read the letters of X. I had set the resolution very low because I had performance problems with rmvb playing over the lan… so I set the resolution to 1280×1024 (through xbmc), now I could read the context menu, but when I started minecraft, I had two windows, one with black screen with the window frame, another with the minecraft screen outside the first one, without any frame, but not centered, I could only see part of it.

The solution was to setup the resolution to 1920x1080p. The Problem is that minecraft work on the GPU so it read the resolution of the TV directly. I calculated that the middle is, but it is not the middle of X resolution. Sync the both and the window are one over the other.