QSYS Custom component not found

Putting files into the .qip file is the same as adding it to the Quartus project directly. That said having the .qsys file as a source file appears to be working now since I saw someone do this the other day (you replied to a post that is over 2 years old). I agree you are running into something else. When you added your components were you creating them in component editor during the system creation or were they created and already on your drive? If it's the latter then what was the location you used? When you put a /ip directory under your Quartus project and open Qsys, it automatically looks there for the IP which is why those cores showed up after you added them to the /ip sub-directory later. If I recall it looks in /ip for any .ipx or .tcl files and it also will recursively look one level deeper for the same files.