Hi:
I figured it out. It was not specific to my PC at all. It was specific to a set of sequence files.
Many of our sequence files have a function call in the SequenceFileLoad sequence callback. This function call is resetting the working directory. This function only runs in the operator interface (Precondition IsEditor==FALSE) which is why it worked fine for me in the editor. Once I unloaded all sequence files from the operator interface and then started it using the shortcut, everything worked fine. As soon as I load one of these sequences, the Open Sequence File path goes back to c:\ though.
I'll try and get the function call modified so that it resets the working directory back to default before exiting.
Thanks,
Dave