When you use IR Learner with the UCM/USB you need to detect the COM port assigned to the UCM, in Control Panel > System > Hardware > Device manager and Com Ports. You should be able to see a device associated with the USB Port. Select that COM port in the IR Learner.
The IR learner is a different application from Comfigurator and it does not use the same connection method
Just want to add that there is a known issue regarding IR Learner in Comfigurator 3.1.1.
See the link here.
Please download the latest version of IR Learner (with 32 COM ports supported) from here. Unzip the file and copy to to the Comfigurator folder, normally located at C:\Program Files\Cytech\Comfigurator 3.