Since the last time I have installed HiJack, I have installed Microsoft Activesync (program used to sync Pocket PC with computer) and am not sure if that is causing it.
That is possible if ActiveSync uses the serial port. Please try disabling the ActiveSync software.

Also, my logoedit files are stored on a different computer (accessing them over the network)....do the files need to be installed locally?
I do not know. Please try copying all files (all logoedit files as well as the kernel you're trying to install) to the local computer and see if that works.
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Tony Fabris