Why you think this is a "problem" ? ATA is listed as a valid operator for LIRF with the same score (4) as ADR so, if you sometimes see ATA, it's entirely normal and GSX is working correctly.
If you don't want to see an operator anymore on a specific airport, as explained both on the GSX manual and the PaintKit documentation, you can act on the Couatl.icaoprefixes for all the vehicles, in the [fltsim] section related to the ATA repaints, and reduce the score for ATA at LIRF, for example by removing its ICAO from the list.
