My new folders are not visible in Finder

New folders (generated by a application, SABNZB+, that runs in the background as a web service) will only show up in Finder once I have run a search in Finder and are not visible before. I have tried a disk repair and a permissions rebuild.
Any ideas anyone?

Yes they do, no problems there.
I am starting to believe it might have to do with the fact that the folders are created by an unarchiver that reassembles files after they are downloaded from my newsgroup. The strange thing is that there never used to be a problem, it started somewhere around the second update to mountain lion. But it could also be a new version of the application SABNzb+, I am not sure.
What is also weird is this: I can find the folder when doing a search in Finder, then open the folder, all files are there and the folder is then visible normally.
Edit: The files are reassembled by the unarchiver on the main Macintosh HD, then moved to a different volume and deleted from the originating volume.

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