Does the duplicate remain if you save the file, refresh the webpage, and load the program again?

I've had a missing Setup block before, but not a double Setup block. I fixed the missing one by modifying the m5f file in a text editor to add the necessary code back to the file. I used a blank file with just the Setup block as reference. Perhaps you can do something similar to find the duplicate code?

If you can't figure it out, post a link to the file and I'll have a look to see if I can fix it.