Played with those a little bit last night. First thing that threw me off was that the original files are 32bit float format dumped from a DAW. The older software (Audio DiffMaker) didn't recognize that at all, DeltaWave did, but didn't play nicely with my audio interface (seemed to want to send 32 bit audio to the interface, even though it should be advertising it is a 24 bit device).
Eventually got them both working well enough, and DeltaWave seems to do a better job time aligning. Even after time and amplitude aligning, the best null achieved was about -55-ish dB.
Listening to the amplified difference there did not seem to be noticeable distortion, frequency response changes, etc., so my preliminary guess was that the playback was started at slightly different points in the original source, that some amount of compression was still being applied, and that the interaction between attack and release time of the compressor meant that there were
very slight differences in gain at each point in time in the resulting files.
Of course if rjb5191 says that the compressor was off, and the unit was only being used as a buffer amp, then that hypothesis would be right out the window.
I did listen to the files, of course, but I could not hear the differences rjb5191 described.
If anyone wants to do some blind checks to see if you can identify the files without knowing what you are listening to this ABX playback and testing tool is handy:
Lacinato ABX software
tutorial on using Lacinato ABX