I had the same problem you describe working on an AC 11 Teamwork file ... unfortunately i never got to the bottom of it (moved onto another project and AC12). This was a while back - can't tell you the build but i don't think it was the latest.
I just created a new file from the default AC 11 template, created 2 slabs (one on a hidden layer) and published as a Multistorey MOD. Opened the module and the slab on the hidden layer was there. Did the same in AC 12, same result.
However the above works if i save the MOD as Current Storey, rather than Multistorey. Didn't try publishing a storey range but i imagine it would have the same problem.
So something is broken.
cheers,
Owen Sharp
Design Technology Manager
fjmt | francis-jones morehen thorp
iMac 27" i7 2.93Ghz | 32GB RAM | OS 10.10 | Since AC5