the dock from the computer almost certainly was not overwritten.
unlike similar programs, LBC can switch between different user files that describe docks.
this affords a lot more flexibility, but it does lead to some real confusion sometimes when someone launches LBC and finds that their nodes have "dissapeared".
so i'd like to suggest that probably what happened is that your LBC opened one file when you expected it to open another. you can browse to the .MCF file which is the extension used for node definition files. Search for such files on your hard drive or usb to find them.
now to run LBC portably, create a file called ConfigDir.ini in your USB launchbar commander directory (i will start including this in future releases), and add the single line to that file from notepad or similar plain text editor:
that will tell LBC when run from the usb drive to store all settings in that same directory, and is the way that all of my programs are configured to run portably.
let us know if you get it working and find your original .mcf file. feel free to contact me directly if you need more help (email@example.com)