Humans normally the first culprit, yes.
Make changes, export.
Then go back to make even better changes and forget to export.
Another thing to check. The FTP/HTML transfer is not properly setup when using a QUICKSTART, which means you can download a new file as many times as you want (html) when 99.999% of the time you would rather get the "no new file message" when you try it a second time (ftp).
If you download, make a bunch of changes, and export (all properly done) but then happen to hit download again, you essentially start all over again and must retrace every move before exporting (properly again) that next time. Easy to forget one or two.
I've done both. 
Not often, thankfully.
By the way, the cure for the HTML/FTP is to have the Commissioner post his/her GMaccounts data file, which will have proper settings.