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I had 5 plugins with updates. After updating all of them through the Available Updates tool they disappeared from the Network Plugins page. I received errors like this for all plugins:

The plugin custom-post-type-ui/custom-post-type-ui.php has been deactivated due to an error: Plugin file does not exist.

The folders still exist in /wp-content/plugins/

When I deleted the folders and uploaded them through FTP they do not appear on the Plugins page. When I install them through wp-admin I receive this log text:

Downloading install package from http://downloads.wordpress.org/plugin/custom-post-type-ui.zip…
Unpacking the package…
Installing the plugin…
Successfully installed the plugin Custom Post Type UI 0.7.1.
Network Activate | Return to Plugin Installer

But when I click Network Activate, I receive this error:

The plugin does not have a valid header.

This happens for all 5 plugins and only happened beginning today.

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I have this exact same issue, seemed to come out of the blue. Did you manage to resolve it? – jsims281 Sep 13 '11 at 10:48
I'm having the same issue, still no solution. – drtanz May 8 '12 at 21:08
up vote 2 down vote accepted

We resolved this issue by removing re-uploading the admin and includes folders, although I'm not sure what originally caused the issue.

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To resolve this error The plugin does not have a valid header. you need to check your plugins file, there might be some white space before or after <?php and ?>

Remove those spaces, then the error The plugin does not have a valid header. wont display

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