When photon-counting detectors are calibrated in the presence of a background signal, deadtime effects can be significant and must be carefully accounted for to achieve high accuracy. We present a method for separating the correlated signal from the background signal that appropriately handles deadtime effects. This method includes consideration of pulse timing and afterpulsing issues that arise in typical avalanche photodiode (APD) detectors. We illustrate how these effects should be accounted for in the calibration process. We also discuss detector timing issues that should be considered in detector calibration.