I'm guessing you DL'd the compressed version of the game. There's some weird voodoo used in that version that changes how the sprites are displayed so the patch is not compatible with that version unfortunately. I'll add a note about that to the post.
EDIT: Alright I THINK the offset issue is because the compressed version uses unencrypted images by default, while the images in my patch are encrypted (like they were in the original version of the game). Normally, when you apply my patch to the regular version of the game, the images files would be overridden (for example file www/img/pictures/00_messe.rpgmvp), but because the compressed version uses unencrypted image files (www/img/pictures/00_messe.png - note the filename extension) the image files don't get overrided, but instead the new files are added alongside the old ones, so the game will still use the sprites from the compressed version. You COULD use the rpgm decrypter by Petschko to decrypt the image files in my patch, but that's probably a hassle too big for most folk
TL;DR Save yourself the trouble and just DL the regular, non-comprossed version of the game if you want to play with upscaled sprites.