atlon, Clownboat - when you say it recognizes the files what do you mean?
Do those files appear in the "File Manager" tab in the options screen?
No. The files don't appear in the File Manager, or in the "Unrecognized" list in the importer within MP. I watch the importer as it hashes the files and then matches them against AniDB. But for some reason, a group is not created for the files and they seem "invisible" to the plugin from then on.
To test it out again, I just imported a folder containing a bunch of series in subfolders. In the end, a few files were unrecognized and showed up as such, but only 2 series out of several dozen appear in My Anime and in the Manager tab of the config. When running the importer again, the "missing" series are ignored; the files do not get hashed or added.
Which series show up and which become "invisible" seems somewhat random, as I have gotten different results from importing the same set of files.
Can you attach your MyAnime2.log file if possible?
I had the same thing happening once, when my database was in an incorrect format (After using a beta version the version numbers was updated, but not all new fields where added). In that case an AnimeEpisode record was created (so the files weren't listed in the file manager tab) but there was no AnimeSeries or AnimeGroup record (so the series don't show up in the plugin).