Does anyone have any idea why it would do this?
You are already using a clipping or blending feature inside the group whose appearance cannot be retained otherwise. Most likely you will have to do some re-arranging of the structure. Certainly you can also get there by cleaning up and e.g. unifying overlapping anchor points or exapnding appearances of some items. Depending on what the output is for, you may get away by using your shape in inverted form as a conventional cover on top of everything. Really depends.
Unless this has changed in later versions, if your Clipping Mask consists of separate paths, select them and Object>Compound Path>Make.
Sounds like problems with the ordering of the layers, if you flatten the artworks/layers in steps you will probably see where the problems are.
Ensure you work on a copy file first!!!