In terms of clipping masks... Groups don't mask.... paths mask.
(Note Opacity Masks are different)
What happens when you use a
<Group> as the top object when creating a clipping mask is that each path within the group is defined as a clipping path and then they are combined essentially into a compound path and the group becomes a clipping region of sorts. Path interactions are similar to selecting everything in the Group and using
Object > Compound Path > Make. This is often not the appearance one wants for the mask path.
Since you already have a group of compound paths, I'd guess that this conversion by the clipping mask feature is altering how those
several compound paths interact with one another and that may be causing an undesirable mask.
It's best to create clipping masks with only paths or a single compound path. Using a
<Group> often results in unexpected masking.
The easiest solution is to change the
several compound paths into a single compound path. Then you will be able to use that compound path to create the clipping mask for the group below it.