We're experiencing the same problem in ArcGIS Pro 1.3: oddly enough, our "GIS" folder shows up just fine, but a folder named "Workspace" (containing user workspaces) is missing instead. It doesn't contain any "arc.adf", just MXDs, subfolders, and some logs and indexing files.
We've had to work around the problem by either typing the path into the address bar, or adding a connection to a subfolder. If we add a connection to the parent folder, though, it's still missing in the Project pane, and we can't add a connection the "Workspace" folder itself.