A variety of GaN epilayers, grown on 6H-SiC substrates using different growth conditions, have been studied using variable energy positron annihilation spectroscopy. In the S-E plots, a peak structure in the S-parameter is seen which is related to the GaN/substrate heterojunction. The position of the peak is found to be much closer to the sample surface than expected from simple mean implantation depth arguments. This anomaly is attributed to the fact that there is a rectifying potential step that prevents diffusing positrons in the GaN from entering the SiC substrate. This effect has been successfully mimicked by inserting an artificial electric field into the thin interfacial region in the VEPFIT analysis.