Just remove the .cue extension from "\console_computer\ignore_extensions.txt" file before creating a games list.
Be aware that Emu Loader have a "use .cue" button in the tool bar buttons so EL can generate the emulator exec command line to run the .cue instead of the .bin/.iso file. But the .cue file must be in the same folder as the .iso;.bin folder and have the exact same filename. Also, by removing the .cue file ext from that file will not detect the file of the iso file correctly.
>> or do I have to separate all my .cue files and repoint them to the ISO images
Aren't your .cue files in the same folder as your .iso files ?