I cannot comment on functionality of HyperTerminal (or HyperDooDoo as another Monk has kindly called it), but if you are simply trying to automate a serial communicatino session, you may be better off using a Kermit like application. Likewise, if you are well versed in Perl, look into Win32::SerialPort and you will have FULL control over what happens when (and how).

Finally, if all you are trying to do is to send a few bytes here and there without any serial protocol, you can even open up the Port with this code

sysopen(COM,COM1,O_RDWR) || die "Can't open COM1 $^E";
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and use these commands to write and read to the port

#code to send data to port
syswrite(COM,$string);  #sends $string to COM1

#code to read data from port
sysread(COM,$buf,$length);      #read $length bytes
$received = unpack("C*",$buf);  #unpack them
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Hope this helps.