I encountered this problem a while ago, I guess it might has something to do with the pipe buffer deadlock.
I resolved this with suppressing (actually, saving) the command line output to a file by adding ">> filename" such as: "dir /w >> logfile.txt" "olala.bat >> logfile.txt"
But this method won't show the log output (If I don't want it, I'd already unchecked log output), so I add a [run script] action and write a script to print the logfile line by line.
Hope this helps while they are checking for the problem.
Eric you haven’t really given us enough information to work with. What is the FinalBuilder build number, windows OS & version, and more importantly what does your batch file do? I would suggest you contact us via email support at finalbuild dot com with your batch file and finalbuilder project so that we can try to reproduce the problem here.