An inkjet printer forms low and high area coverage test patterns using inkjets in a printhead. The printer identifies process direction offsets for the inkjets in both test patterns using scanned image data of the printed test patterns. The printer identifies a level of cross-talk in the printhead with reference to a standard deviation difference between the process direction offsets identified in the low area coverage and high area coverage test patterns. The printer generates a recommendation for an operational configuration of the printhead based on the identified level of cross-talk.