X-Plane should see them whether you start with them plugged in or plug them in later. Please file a bug report about this here. We will need complete log.txt files from both situations. So, in your report include a copy of the log.txt from the main folder by:
Starting X-Plane with them plugged in (I assume this is the way you usually start) then quit. Please rename the log IMMEDIATELY or X-Plane will write over it.
Start X-Plane again then do the unplug, wait, plug in process you have to do in order to use your equipment. Quit & rename that log.txt file as well.
Then attach both copies of the log.txt to the bug report form and list all the steps you take to see and then fix the problem.