The behavior of the Command Window in R2011a seems to have changed so that it doesn't automatically scroll to the bottom on a line feed if MATLAB is busy.
If I run this in my shiny new MATLAB 22.214.171.1245:
clc, for a=1:100,fprintf('%i\n',a);pause(0.1);end
... the counter will just run down to the bottom of my CW and then keep going while the vertical scroll bar grows. My dull ol' 126.96.36.1994 (R2010b) and my linux version (either release) don't do that; there the command window scrolls down on a line feed. Is that intentional new behavior or a bug? If it is a feature, how do I control it?
Edit: Okay, I'm pretty sure it's a feature. If whatever is in the loop isn't terribly computationally expensive and not calling system commands or mex code, it actually lets me choose between freezing the scrolling or letting it go by moving the scroll bar (i.e., if the scroll bar is at the bottom, it updates as it used to). Seems like this just doesn't always work.
Edit2: Also, that trick to control it only works on Windows 7.
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This answer only helps you if misery loves company. I've noticed the same command window scrolling differences, although I have not tried to pin down the exact circumstances.