Starting with the 2006-2007 season the NBA changed the tiebreakers so the 3 division winners do not automatically get the top 3 seeds. Instead they where reseeded with the top wildcard to determine seeds 1-4. The site does this part correctly.
Starting with the 2008-2009 (?) season they added the stipulation that when reseeding the top 4, a division winner always takes precedence over the wildcard with the same record. I don’t do this. And it affects the current standings.
Jeremy Halperin pointed this out today (thanks Jeremy). I’m working on fixing it, more to follow.
Update: I believe it is fixed.
Here are the 4 affected teams, using the 50/50 version: