There is indeed some confusion on this issue. The issue has even been submitted again after this one was closed:
http://projects.blender.org/tracker/?func=detail&atid=125&;aid=18689&group_id=9 (also closed)
Maybe I can clear a couple of things up:
Console.app / system.log is simply a bad place for this sort of output. The system.log is a useful place to see what your computer was doing at any given time, why an app crashed, etc. However, this log contains data from any app / process, and is continuously written to disk (as a large file including the backlog).
This means that to see things in the log, the log process has to process them first. Naturally, if this wasn’t done intelligently / with a buffer, every process would write to the disk several times a second - very bad for performance. So, the logging is
done in the background and asynchronously, no promises made on when precisely things will appear, just that they eventually will, and in the correct order.
If you program your own app in XCode, and dump stuff to the log, you have the same issue - you can get the output in system.log, but you can’t dictate when it appears. At least, if you try to, performance suffers. So, in XCode, use the debugger, which has a terminal directly showing output without having to write to the log. Memory vs. hard disk / focused task vs. general system tool.
We can do the same for Blender.
I found out how, and have put together sort of a walk-through on how to get a double-clickable application with the right icon that launches a terminal output window, here:
(It takes all of two minutes).
The issue remains one of education - “console” is sometimes used interchangeably with “terminal” or “shell”, to describe the output window you see on e.g. Windows. Yet, on OS X you decidedly want a Terminal window, not a Console. (It doesn’t help that Ton apparently mistakenly swapped the terms, in the comment above).
Now, this should be made clear somewhere, and we should spend some energy educating about this issue (since the other option - making it work well in console.app means pleading with Apple, not Blender foundation.)
Except, as Campbell noted when he closed the other bug - Blender 2.5 has a built-in console planned. Much nicer, and the same for all platforms. So any solution we get now, will be moot in 2.5.
Hope this helps.