Thanks to a nice MS person we where able to solve the encryption problem. The steps that we needed to take where these:

Find tou Office setup.exe and run it with /admin switch

setup.exe /admin

This will start the Office Configuration Tool.

If you have previously configured setup customization files the you can edit those or create a new customization file.

After the settings part has loaded you should go to

Features\Modify user settings\Microsoft Office 2007 System\Security Settings

You can find there two lines that start with “Protect document metadata …”. Set those lines to Disabled
and save your configuration file File->Save.

The tool will create an MSP file for you that is needed to run on every computer where you want to work with Sharepoint and Office 2007.

I think you can deploy this MSP file with an script using msiexec and Group Policy.

Hope this solution can help other people but it definitely helped us.