1: The SQL Server Compact Toolbox now longer works after upgrading to Windows 8.1
2: Entity Framework based SQL Server Compact solutions no longer work after upgrading to Windows 8.1
When upgrading a machine that already has SQL Server Compact 3.5 SP2 and/or 4.0 installed, the DbProvider registration, which is stored in machine.config is broken, probably due to the fact, that a newer version of .NET Framework is installed (version 4.5.1) which simply overwrites the existing maching.config file. Both the SQL Server Compact Toolbox and Entity Framework depend on this registration.
The fix is to repair/re-install SQL Server Compact 3.5 SP2 and/or 4.0 SP1, both versions are fully supported on Windows 8.1/Windows Server 2012 R2.
You can download 3.5 SP2 from here: http://www.microsoft.com/en-us/download/details.aspx?id=5783
You can download 4.0 SP1 from here: http://www.microsoft.com/en-us/download/details.aspx?id=30709