I've been having this odd issue recently where my command line screens will basically lock the programs writing to them until I give mouse focus to the DOS window and then perform some keyboard action.
So, for example: I'll start a Tomcat instance and at some point, it simply stops updating -- I hit reload and nothing happens, nothing outputs to the Catalina window. Or, I'll check out something from SVN and it will appear to lag, but as soon as I interact with it, the lag stops.
Edit
My aplogies, I used the word "screen" when I meant "window" (that is fixed).
The command (to start Tomcat):
C:\liferay\binaries\liferay-portal-5.2.3\tomcat-5.5.27\bin>startup.bat
The command to checkout a repository (in Cygwin):
$ svn checkout <repository>
To the requests to change the operating system, I say "no". At no point have I mentioned which operating system I was using, I simply stated that I was using DOS (common use implies MS, but the comments stated that I have incorrectly stated which OS I was using). Since this problem has never exhibited itself in anything other than that environment, it is not intuitive to say that this is a Windows problem.