Figured it out, it was indeed a bug (and I have filed one).
A colleague of mine managed to flawlessly index the Github project which resulted in :
Indexed 'src' (20 sources, 1,061 headers) in 43.46 sec: 86,471 declarations; 231,728 references; 0 unresolved inclusions; 12 syntax errors; 592 unresolved names (0.19%)
He was on a Fedora distribution with its default package of Eclipse Juno CDT. This meant that he was using :
Eclipse C/C++ Development Tools
Version: 8.1.0.201206111645
which is not quite the same as the standard Juno CDT download :
Eclipse C/C++ Development Tools
Version: 8.1.1.201209170703
I checked this workaround on my Ubuntu system (12.04 LTS) by installing Classic Juno along with CDT 8.1.0 and the indexing/parsing works all right now.