Here's the answer from Noel at Cakewalk. I followed his advice and all is well. As a bonus, this version of the adapter does scan faster.
From Noel:
Are you running SONAR 4.04? Check the folder defaults settings in the VST wizard.
You probably have the default set to disable plugins. So when you rescan all new plugins are disabled by default if so. If its set to disabled, just toggle this setting in the defaults and this should stop happening.