I'm not sure whether you've seen this one, from the "sound of DSD" thread:
By the looks of it the offending samples differ by time delay (non-integer number of samples) only. I tried matching them up in Audacity manually and had to resample to a 1 MHz sample rate to even get a -60 dB null. Still, I would imagine that dealing with arbitrary time delays is kind of basic and important.
I did see it, and responded in that thread. The main problem with that test was that the two files were too short and contained fully periodic material (a single sine-wave). DeltaWave tries to compute clock drift, variable group delay, jitter, etc., all of which requires quite a few more samples than a few seconds. I never measure with less than 30 seconds, but with lower sampling rates, such as 44.1k, I'd say use at least a minute.
Generally, music or noise test signals are preferred to sine-waves, since two sine waves can align perfectly at thousands if not millions of places, and DW has no way to pick one over the other. When using periodic signal, there is a setting that should help and needs to be turned on: Measure Simple periodic waveforms. This attempts to deal with exactly this issue.
Speaking of time delays, DeltaWave not only measures and corrects delay to much less than 1/1000 of a sample accuracy, but also measures and corrects non-linear phase effects and clock speed differences.