When did you run the downloader? - The previous topic in this forum is that the 4ed files can't handle the compendium as it exists on June 2nd, but an update is coming as soon as possible.
I'm not too familiar with the 4ed files, but you may have downloaded only the "Download data (no D&D insider account)" data (option 1 in the downloader), rather than "Download data (with D&D insider account)" (option 2 in the downloader) - that's another thing to check.
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