Daniel,When you install SQL Server 2005, SQL Server also installs new VsPackages into Visual Studio and has to execute some command line options to install the packages. The installation probably launched Visual Studio with a different set of environment parameters causing the error in the StrataFrame menu. You've probably noticed the new VsPackages on the Visual Studio splash screen when it starts up (SQL Server Analysis Services, SQL Server Integration Services, SQL Server Reporting Services).
Since you can still get into the StrataFrame menu, and both the DDT and the BOMapper are launchable, you should be fine; it was most likely a one time error that came up when VS was launched during the install.