launch instance of Microstation with correct workspace/workset

i have a standalone app that will launch a instance of microstation and pass in the -WK parameter for the workspace name, the -WW parameter for the workset name and the -WA parameter for the startup app.

it works great..most of the time. here is what i have found out

i have my workspace over in the Custom config side (using the ConfigurationSetup.cfg file and the _USTN_CUSTOMCONFIGURATION variable)

I have found out that it will only work if the last used workspace/workset is over on the custom config side of things. 

so for example if i launch a bentley delivered workspace to go through some training and then i close out of microstation and then i run my stand alone up, when it launches the background instance it cant find the startup app because it couldnt find the workspace/workset. 

its like its only looking for workspaces within the last used configuration branch. see image below for what i mean when i say configuration branch.

So the question is how can i reliably launch my background instance to use the correct configuration?