1. Don't Hot-Plug the brainstem! Hot plugging it causes it to hiccup the micro controller and causes weird results.
2. If you do Hot-Plug it and you want it to behave normal, do the following:
Take a Jumper and short pins JP1 A2 and B2. Be very careful when you do this. (Don't randomly short out everything with tweezers.) Shorting A2 to B2 will put the DSATX in the Reset state and reset any weirdness you created from hot-plugging your brainstem. You must then un-short it for it to come out of the reset state.
3. You must enable writing if you are going to change parameters
The when you want to set paramters you must (E)nable writing first. A capital E will then ask you if you want the DSATX to burn the EEPROM with new settings as you type. Yes. Then you won't get line feeds for every key as your typing an S command.
4. F and O will turn on and off the Feed Diagnostic Output. If you type, you should see an echo. That means you have hyperterminal setup right.. It you type and you don't see anything, your not setup right. 9600 baud, 8 bits,1 stop bit, no parity, no flow control.
5. The brainstem is plugged in right if it goes into the 4 pin connector without trouble. The circuit board of the brainstem should not hit the white housing of the connector.
FYI:
Hot-Plug means connecting the brainstem connector to the DSATX while there is 12V on VIN. When ACC is has 0V and VIN has 12V, that IS a Hot-Plug. You can also use use needle nose and pull the fuse (Or disconnect VIN from the battery) rather than shorting the pins to correct the problem.
You can disconnect the VIN from the battery (for 5 or more seconds) and it will have the same effect as the reset.
Here is a youtube:
http://www.youtube.com/v/y9cSO2sNrxk