Loading Encoder firmware with Hyperterm or Minicom

<P style="MARGIN: 0px">It may (very rarely) happen that uploading a new firmware revision with the supplied Roborun utility doesn't work. Below is a description on how to upload new software using Window's Hyperterm utility. These steps can be adapted to Linux/Minicom.
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<DIV><FONT face=Arial size=2></FONT> </DIV> <DIV><FONT face=Arial size=2>- launch the RoboteqCOM1 hyperterm</FONT></DIV> <DIV><FONT face=Arial size=2>- click on the disconnect button (looks like a phone off hook)</FONT></DIV> <DIV><FONT face=Arial size=2>- select the File:Properties menu</FONT></DIV> <DIV><FONT face=Arial size=2>- click on the Settings tab</FONT></DIV> <DIV><FONT face=Arial size=2>- click on the ASCII setup button</FONT></DIV> <DIV><FONT face=Arial size=2>- type 10 in the Character Delay box (this will cause the data to be sent to the controller to a slower rate to allow for the programming delays)</FONT></DIV> <DIV><FONT face=Arial size=2>- Click OK, OK.</FONT></DIV> <DIV><FONT face=Arial size=2>- click on the connect button (looks like a phone on hook)</FONT></DIV> <DIV><FONT face=Arial size=2>- press the Caps Lock button</FONT></DIV> <DIV><FONT face=Arial size=2>- press the controller's reset button. Type the letter Z several times as you release the reset button. You should see "ISP" on the terminal window</FONT></DIV> <DIV><FONT face=Arial size=2>- select the Transfer:Text File menu</FONT></DIV> <DIV><FONT face=Arial size=2>- select the encoder firmware file</FONT></DIV> <DIV><FONT face=Arial size=2>- You will then see a series of + characters followed by a new line every 10 seconds. Wait until it stops (there will be 4 underline characters). This will take several minutes.</FONT></DIV> <DIV><FONT face=Arial size=2>- reset the controller.</FONT></DIV> <DIV> </DIV> <DIV> </DIV>

We tried this and here's what happened:
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<P style="MARGIN: 0px">1. Attempt to use Roborun failed, since the update controller utility refused to load the file.
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<P style="MARGIN: 0px">2. We then set up hyperterm and successfully updated the encoder software to 1.7 - appeared on reboot when we connected to the controller
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<P style="MARGIN: 0px">3. We FAILED to update the controller software using the same method we used to update the encoder software. When we tried to send the file, the system ignored us completely. So now we have a encoder software at 1.7 and an controller at 1.6.
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<P style="MARGIN: 0px">4. The resulting system WILL NOT go into "constant position" mode, even with optical encoders attached, functioning, and parameters set.
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<P style="MARGIN: 0px">Suggestions on finishing the update using Hyperterm would be appreciated.