The patch added in bug #116629 works, but it's a little sloppy, since it creates a small memory leak. I have a slightly more invasive patch that fixes the problem correctly. Also, I suggest marking the original 1.55 ~amd64, or even -amd64, since it just doesn't work on a second run without removing the config.
Created attachment 84537 [details, diff] fixes strings in functions for locating config file
Created attachment 84538 [details, diff] tested patch I forgot to actually test the patch before submitting it... Must be late. This one is tested.
Memory leak should be fixed in games-arcade/tomatoes-1.55-r2 Patch is not exactly the one you posted, but thanks for pointing out the problem