You have to be doing something wrong, and it sounds like most likely it has to do with the ASCII/Binary conversion. All .tar files have to be transported _all_the_time_ as Binary. The .pm files have to be uploaded as ASCII, although transport as binary really won't hurt them, it will just confuse the FTP program.
I upload .tar files to my Plugins/Uninstalled directory all the time, without the problem. As long as the file is transferred in binary, the permissions are 777 and the name of the .tar file matches the .pm file, things work fine.
I've had no problems with this on a half dozen sites for the past 3 or 4 releases.
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