You can change this setting this under the Tools->Options menu item. Scroll down to the Projects and Solutions and click on the Build and Run setting. In the resulting right-hand pane use the bottom pop-up and change the output verbosity to Detailed as shown in the Figure at the left.
Now rebuild your solution, click on the Output window (use the View->Output menu item if you don't have it showing) and you will have all the data needed to solve the problem. I just grabbed all the data in the window and threw it into my favorite text editor and searched for conflict. I quickly found the following line
There was a conflict between "System.Data.SqlServerCe, Version=126.96.36.199, Culture=neutral, PublicKeyToken=89845dcd8080cc91" and "System.Data.SqlServerCe, Version=188.8.131.52, Culture=neutral, PublicKeyToken=89845dcd8080cc91
Now that I can do something about. All along I was assuming it was one of my .dlls and it turns out it's one of Microsoft's. This explains why the assembly dependency graph didn't help me, I hadn't added this .dll to the diagram. The fix was simple, I just removed the reference to this .dll and re-added it, no more warning and now the correct version of the assembly is getting used.