Ok, we have a look at it and, in fact, it's not that Virtual airlines are not working, they are a bit confusing...
First, when you create a custom operator, you MUST "Restart and rebuild the airport cache". The name of the option is a bit misleading, since it used to be only an "airport" cache but now, since the number of models has grown a lot since GSX came out, it's also a "model" cache so, whenever a new model or repaint is installed, the cache must be rebuilt.
And, the custom operator MUST have its atc_parking_codes = XXX line, where XXX is the same name of the custom texture itself.
And, it's not explained but, you should always create a custom operator starting from the "handling" section of the GSX parking page, not the "catering" section, otherwise the Virtual airline override won't work, since it's supposed to override the ground operator. This might be confusing, and since some would probably like to have a different override for the handler and the catering, in the next update we'll add TWO separate override, one for the handler and another one for the catering.