I'm at work, so i cant give exact details, but i do believe lincity has to be run from its installed directory. Check /usr/games ( i think it installs there ). If its there in terminal try this:
cd /usr/games
./lincity (or whatever the executable is called)
If it runs, then edit the jwmrc file and add something like this to the execution line:
cd /usr/games && ./lincity
If that doesnt work i'll try to boot mine up when i get home to give you the exact specifics. Some games are picky like that. Most any other software loads without the need to run it from its installed directory.
Cheers.