I have the same problem. This is with common plugins like Akismet or JetPack.
Installing the plugins works fine. But when I want to active the plugin, I get the message "The plugin does not have a valid header". When I go to the Plugins tab, it does not list any of the installed plugins. When I look into the "wp-contents/plugins" directory with a FTP client, I can see the plugins are installed and have the correct privileges (755).
I have tried re-installing WordPress 3.4.1 manually. But this did not help.
If anyone knows a solution, I would be happy to hear it?