Nope -- you didn't go astray during the backup... you went astray slightly with the scripts, but that's OK! (And good news.)
The scripts listed in "open scripts" are *all* the scripts, not just the one you're running. If you open the script pop-up, and then choose "edit selected script", then click the tab for "included scripts", you'll see the two scripts that are actually included in Backup -- all files.
In any case, you really sound all set! If you want to look at the files that are excluded, as before, just open the folders listed in the message above, or in the script. But, I truly think you're just fine...
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--Dave Nanian
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