Not sure which saves you refer to, since you're quoting kd3, but, unless the "skunked" version significantly changes something about the file structure, it should be compatible, I think.
I think kd3's explanation is probably spot on. You need a config.rpgsave and global rpg.save that have the save files in use. You can either try kd3's suggestion (basically saving on slots so your config file registers them as used, then replacing those save files with mine) or you use the attached config save files from me, which should register all three savegames in use.
EDIT: Simply extract these into the MGA 0.9\www\save folder.
Preferably make a backup of your own first, just to be sure.