First off props to you Roman for a killer app. Very useful.
Next, the question at hand:
Are there plans to fix/change this behaviour? (Make ClrMamePro detect correct CHD's within set zips)
PS. I have verified that CHD with CHDMAN.EXE and it has the correct md5 checksum. Also, ClrMamePro accepts it if I put just the CHD in a folder with the set name.