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If you do the patching yourself, you shouldn't have this problem.
1) Find a CLEAN, <U>unhacked</u> copy of Mother 3 ROM. 2) Download the Translation patch from http://mother3.fobby.net & any possible language you may need. 3) Unzip & use the enclosed patch program on the ROM -- Enable "Create a back-up" option, just to be safe 4) Get yourself a drink & wait for it to complete. 5) Enjoy!
If you do it yourself, it should work OK. However, you may want to check the list of "Good Emulators" on the Mother 3 Translation site just to be sure as those are known to work.
Once you're in the game, find a frog to save... They're camped out throughout the game, including some weird looking ones (like the Magical Butterfrog).