In case anyone else runs into this issue, here's an update. I wrote the logo program directly and received the solution. The Works with Tool is only compatible with .NET 3.5 SP1 (or 3.5.1), and the installed level needs to be set to that -- no older will
work, and having .NET 4.0 installed doesn't include the necessary functionality.
Windows 7 comes with 3.5 SP1 out of the box, but Windows 2008 R2 only comes with .NET 3.5. I needed to go to the Server Manager and add the ".NET Framework 3.5.1 Features", and then the tool loaded without problems.