Can this issue be replicated using the same DotNow/SDcard but a different host PC? The Exfiltrator PC program requires keyboard input, by the user, to provide the COM port number as a string. In the past, I've encountered difficulty with COM port numbers being enumerated as "COM 1" or "COM1" on different versions of Windows .NET -- currently my Win7x64 box requires "COM 1" with a space character. If the issue is related to the "COM #" string input, the bug could also be due to using alternative input methods or international keyboards. A work-around may be for us to actually enumerate/show the active COM ports to the user and ask the user to select the correct COM port (behavior similar to MFDeploy), or skip the user and automatically connect to the COM port if there is only a single COM port available.
When Jin arrives, it may also be advisable to note the exact SD card model and serial number, and make a copy of the full SD card using the 'dd' utility on a *NIX OS.
-Mike