I am trying to write a batch file that will load into hyperterminal so that I can send commands through the terminal with some being delayed to wait for a response from the machine I am talking to. The commands are simple text commands such as "move a=2000" which moves the a axis to 2000 encoder counts. We currently have it reading in these commands from a text file, however we have to pause each line 10 seconds because we cant specify which line needs to pause while other lines don't need to. Can anyone point me to the right direction?

You can't use HyperTerminal to achieve what posted as that application is not command line driven and so can't be embedded in a batch script. If the machine response is straightforward for each line/command sent, may be I can give you what fits your needs. Please, contact me by e-mail, specifiing exactly the general commands and responses format. The above only if the communications are performed through a serial RS-232 port (COMn).