Here:
http://www.barra.com/research/fundamental_detail.asp
it says that your P/E Ratios (for indexes), Incl and Excl negative earnings, are the SAME 
... except that "Incl Negative"  includes negative earnings. 
I assume this means that, in BOTH cases, the market caps are included for ALL companies in the index 
and only the total earnings is different. (That's what your description seems to say. Am I right?)