I don't guarantee this is the right answer, but when I see one of my script files missing in the list, invariably I've found some syntax error in the script and after correcting it, it again shows up in the list. My guess is that the error is too much for Firebug to parse as an error and so it just rejects that file. SOMETIMES you can make it show up just by refreshing a few times. Again, another guess here is that refreshing the cache and/or giving Firebug a couple more passes at parsing the same file enables it to recognize it as a valid .js file that just needs a syntax error corrected.
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