I cant really post any code because its work related and cant show any code. But ill try and recreate what happens abstractly.

open2(read,write,program);
for (executes about 6000 times)
{
              print write $cmd;
              #This works fine and dandy until about usually 3500 iter
+ations into the loop, and its the same command everytime.  Sometimes 
+I even get to 5000 iterations into the loop before the program hangs.
}
[download]

Whats weird is if I open up the program manually and execute the commands that my script does by hand everything works fine. This is why I thought it was some kind of Windows buffer error.