I also came across this issue. In my case, I intentionally did not have a Catalog selected for the Order Guide as a way to prevent users from searching for it in the catalog. 

I added the Order Guide to the Service Catalog catalog (which is the only one we have) but the Order Guide still did not show when I had the portal of Employee Center selected in the ATF Open an Order Guide step. I changed my portal to Service Portal and then my Order Guide appeared.

It seems that Order Guide field applies some querying parameters to it's search, which I'll assume is what's causing the issue.