Since I can't reopen
http://www.jetbrains.net/jira/browse/IDEA-16364
I created this issue.
Dimitry Jemerov mentioned there:
"The autoscroll works if your caret is exactly at the end of the output."
The bug is, that the caret does not stay at the end of the output. It gets up one line when reaching the bottom. After that it dows not scroll anymore.
This is still present in 7.0.2 (b7590).
Its really annoying.