Unfortunately, I don't know if there is any solution for this. Several people reported problems using disk made saves with the download version of the game (either unable to load, or they would load but then saving would be disabled). An unofficial patch to add download files to a disk install would also potentially have this issue.
Did you try manually setting the resolution in the config.div file? (widescreen and higher resolution support being the main update in the download version) The disk version game should be fine at other than supported resolutions, but opening the auto map can cause the game to crash (the frequency of which is system and resolution dependent).
