You're using custom design / css / masterpage. After you sync a workspace, the design is lost and even standard SharePoint UI isn't displayed, instead mostly text will be displayed.
This is caused duo to insufficient permissions on /_catalogs/theme/Themed. Customers reported that this could happen, even if the account has Farm Administrator permissions.
You can either correct this manually or ensure that the account used by Collaboration Manager has Farm Administrator permissions + permissions on Web Application policy.
Consider our user guide for detailed description on how to set the farm administrator account. Also make sure that you're using the original farm administrator account as even Microsoft's API only supports this kind of scenario - delegating permissions is not enough: http://help.solutions2share.net/documentation/Collaboration_Manager/2013/SecureStoreService.html