Roman, for the first time I used a datfile created from inside ClrMamePro with mame.exe v0.127 (but I just saw v0.128 is out!).
With it I correctly can see, like you said, all CHD-regions ;-).
Yesterday I ran a full-scan (with all type of CRC selected, decompress etc.) of my rom collection: it took 8 hours and 13 min to complete (my PC is 3 years old)!
More or less like before when I used Logiqx dats that were not XML, excluded the extra time needed for cubeqst.chd.
I'm sure that the scan stopped for checking a long time on every CHD file but at the end, in the log window, I saw that MD5s result said "N/A".
Did it check for any reason only SHA1? Just to know... because anyway now I sure all ROMs/CHD/Samples are OK.
[edit]: I just read again your previous answer and noted that you already said MAME binary doesn't have inside the MD5s CRC values...

Another question:
Compared with Logiqx dat MAME v0.127 the dat created with CMP differs about the "alpha denshi" samples: it says the the old samples are not necessary anymore (8 zips for 8 games, but I suppose they were "fake") and it wants only "alphamc07.zip" samples... which of the two is right? Yours, of course ;-), but why Logiqx dat is different?

Another question:
Is there a way to create, using CMP, a diff dat between two mame.exe versions?

A. Q.:
Can CMP export a dat he created in some kind of filetype? It seems that the dat file created in the datfiles directory is like a placeholder...

An idea:
It would be nice to have a feature to pause a Scan (expecially the ones that you know are long), maybe by creating a temporary file with the results up to that point, and to resume it at a later time, instead of aborting it...

Maybe too many questions?

Many, many thanks for all your work on CMP!!!

P.S.: you were right, I missed a lot!