More than likely it's that you're not placing the correct files on the Kobo. When you download the firmware you download a file named kobo-update-<build number>.zip
You then unzip this file to obtain KoboRoot.tgz, manifest.md5sum and a folder upgrade that contains several more files.
All of these need to be copied to the .kobo folder of your reader.
After the copy your .kobo folder should contain the Kobo root.tgz and manifest.md5sum files, and the upgrade folder that will contain several files.
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