I have been struggling with DGNWS issues also.
I have successfully placed all the dgnws files in one directory ==> Worksets/_DGNWS
I set the following variables in the WorkSpaceSetup.cfg:
_USTN_WORKSETSDGNWSROOT = $(_USTN_CONFIGURATION)Worksets/_DGNWS/
_USTN_WORKSETDGNWS = $(_USTN_WORKSETSDGNWSROOT)$(_USTN_WORKSETNAME).dgnws
I do NOT manually create the worksets. I use the "Create WorkSet" from the WorkSet pulldown of the Work Page.
I hope this helps a bit.