Adaptive psychophysical methods are widely used for the quick estimation of percentage points (thresholds) on psychometric functions for two-alternative forced-choice (2AFC) tasks. The use of adaptive methods is supported by numerous simulation studies documenting their performance, which have shown that thresholds can be reasonably estimated with them when their founding assumptions hold. One of these assumptions is that the psychometric function is invariant, but empirical evidence is mounting that human performance in 2AFC tasks needs to be described by two different psychometric functions, one that holds when the test stimulus is presented first in the 2AFC trial and a different one that holds when the test is presented second. The same holds when presentations are instead simultaneous at two spatial locations rather than sequential. We re-evaluated the performance of adaptive methods in the presence of these order effects via simulation studies and an empirical study with human observers. The simulation study showed that thresholds are severely overestimated by adaptive methods in these conditions, and the empirical study corroborated these findings. These results question the validity of threshold estimates obtained with adaptive methods that incorrectly assume the psychometric function to be invariant with presentation order. Alternative ways in which thresholds can be accurately estimated in the presence of order effects are discussed.