@Jakub:
The differences happened in 1997 and the quick analysis is that some batch files are added by commiter "Perl 5 Porters" and then deleted by both Tim Bunch and Gurusamy Sarathy.
git log -- win32/bin/webget.bat
shows removal by Tim (ohloh sees this commit multiple times, since multiple branches are enlisted, here's one of them
and then, in the wrong time sequence, addition by Perl 5 Porters that ohloh sees; again this same commit is seen multiple times since multiple branches are enlisted in ohloh)
The change by Gurusamy isn't shown. This might be because git log knows the changes were merged but Ohloh was confused or perhaps the git history is confused.
Perhaps the confusion is partly due to the way the repository was committed. But we do plan to improve Ohloh's ability to understand duplicate commits.