This is a very old issue, I've been seeing it on all my macs since forever, first noticed the problem in 10.2 i think. Then later during the 10.3 era I discovered the cause described below, I have reported this bug to apple multiple times, but its not been fixed yet.
As far as I've seen its caused by launching an application that immediately crashes during its first "bounce", it happens frequently when developing apps for example. After a long session of Xcode, I always have to fix the minimize problem by just restarting the Dock.
That is, running "killall Dock" in Terminal fixes the problem, until another app crashes while starting again.
If you don't believe me, it can easily be reproduced by creating a "fake app" that can reproduce the problem at will.
Basically type this in terminal to create a "fake app" on your Desktop named test.app:
Code:
cd Desktop
mkdir -p test.app/Contents/MacOS
cp /bin/ls test.app/Contents/MacOS/test
When you run this app you will notice how a small animation happening in the dock where the app would have popped up if it wouldn't have quit.
That I believe is what "breaks" the Dock somehow, and after that all window minimizations are choppy just as you describe(with window maximizing still being fine).
In conclusion run this in terminal each time you get this problem:
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