Ah ok.
From a quick look, exo should be the creator of a DOS games collection and you can find his dats in pd forum and other places, i remember seeing a topic there about his dats and the usage of other tool different from cmp pro because of some folder problems, maybe you should have a look there to see if it is useful. Anyway by that topic you posted it seems to work fine, if that option is needed by default for you (and other dats possibly) we should not forget about it and maybe have a note about it in our main page also (in FAQ for example, any of you wanting to create or post there feel free to ask me
)
A bit more about the problem discussed there, what Roman said is that in a datfile, when a subfolder has files/folders in it, there is no need to have each folder entry on the zip or described in the datfile, example (should be easy to understand but anyway):
#1
\folder
\folder\subfolder
\folder\subfolder\romfile.bin
#2
\folder\subfolder\romfile.bin
Instead of #1, option #2 should be enough to correctly recreate the exact structure when unzipping the zip file. What did you use to create the datfile? cmp?
I remember back when i started trying to fix tim it had a problem with zipfiles and subfolders and that's how i found this too.
My suggestion is for you to do some quicktests if you can to confirm this, create a dat for that file with cmp, scan it with and without the option and see what are the results, extracting the content to see if something changed and also testing how it works with empty sub dirs since some weird old systems might need/have them.