Many published cladograms report measures of stratigraphic congruence. Strong congruence between cladistic branching order and the order of first fossil occurrences is taken to support both the accuracy of cladograms and the fidelity of the record. Poor congruence may reflect inaccurate trees, a misleading fossil record, or both. However, it has been demonstrated that most congruence indices are logically or empirically biased by parameters that are not uniformly distributed across taxa or through time. These include tree size and balance, mean ghost range duration (gap size) and the range and distribution of origination dates. This study used 650 published cladograms to investigate the influence of these variables on the Gap Excess Ratio (GER). In a range of multivariate models, factors other than congruence per se explained up to 74.5% of the observed variance in GER amongst trees. Arthropods typically have poorer GER values than other groups, but the residual differences from our models are much less striking. The models also show no clear residual trend in GER through the Phanerozoic. Because the GER is strongly influenced by parameters related to cladogram size, balance and duration, comparisons across trees should be made with caution.