We do not require WSUS and EW to be on the same drive. This error is new to us. I would suggest we schedule a GoTo Meeting to investigate this. Can you please send an email to www.solarwinds.com/customerportal referencing this post. It would also be helpful to include your time zone as well as times that are convenient for you to meet.
i got a similar problem. If i try to show the WSUS signing certificate, it shows me N/A in every field. Shouldnt it come with standard WSUS installation?
While you are correct that WSUS already 'knows' to trust Microsoft content, it does not by default know to trust 3rd Party Content. Therefore, in order to deploy 3rd Party Updates, you must add a signing certificate to the WSUS server. That certificate is then distributed to the EminentWare server, any downstream WSUS servers, and also to the end-user clients (so that they know to trust the 3rd Party content from the WSUS server).
These concepts are covered in the Third Party Updates Local Publishing Administration Guide.