I found the same problem with one plugin that I have installed and update regularly on more than one blog; StatPress
The plugin is great, but with rapid development and frequent updates, the inability for OneClick (or the One Click Plugin Updater plugin for that matter) to handle the files being in a folder in the archive is annoying, but it isn't an issue for OneClick, it's for the other developers.
The FAQ on the wordpress SVN does make the suggestion to developers to leave thier files in the root/trunk and not in a separate directory root/trunk/folder. This is because the SVN builds the ZIP file dynamically from root/trunk into it's own folder in the ZIP file.
I found the simplest solution, download the file to my computer, unzip it, move into the plugin directory and ZIP the interior folder.
I then use the new ZIP file with OneClick to install from my local copy, correctly zipped.
Asking to change OneClick, or the SVN for that matter, to alter their methods, because developers can't or won't follow standards, is like asking web designers to build two web pages, one for internet explorer, one for all of the other browsers which are standards compliant...
wait... bad example...