I've long noticed problems with settings in one application, when another is also started (i.e., the Shortcuts added to the Open dialog, etc.), but do not experience this behavior... Due to my not using Startup Suite.
Instead, I use Acad.lsp + AcadDoc.lsp + [SomeCuixName].mnl to load all of my LISP routines, without any issues.
HTH
Moderator: This must have accidentally been started in the .NET forum, can this be moved?