[Johan K]

To clear some confusion, here are the env variables, their default value and what they are used for.

DOM2_SAVE default="." Save directories and the newlords directory are created here. You need write permissions here.

DOM2_DATA default="." Data files, the maps folder and the rawsound folder must be found here. You only need read permissions here.

And Raen your problem with two game using the same save directory seems strange. Maybe one of your shortcuts doesn't set the current directory and thus the old one is still used.