Yes; I just encountered this bug today after starting KSP up for the first time since the 0.23.5 update. It seems that the version of the toolbar that's packaged with DPAI is an older one, and causes compatibility issues for MechJeb. The fix is to download the latest version of the toolbar from this thread: http://forum.kerbalspaceprogram.com/threads/60863-0-23-5-Toolbar-1-7-1-Common-API-for-draggable-resizable-buttons-toolbar. Delete the '000_toolbar' folder that DPAI installs from your GameData folder, then install Toolbar 1.7.1 in its place. You should find that MechJeb works fine after that.
