OK, my LBC files all seem to be located at D:\Documents\DonationCoder\LaunchBarCommander\
That folder contains an .ini, .mcp, .mcf, and .bak files. However while there were several old backup (.bak) files in the Documents directory, most of the backups for my dock are in the Program Files directory, which is exactly where you posted that LBC should not be trying to save files.
Unfortunately I can't find any information regarding where to save what. Also, no place I can find in Options to designate file locations. Looks like the .ini file could do it but I don’t understand all of the coding there. For example, the Form Placement line doesn’t mean anything to me. Surely there is a better way to designate file locations!
Here are the contents of my LaunchBarCommander.ini file:
TBXMRUList.Items=text:"C:\Program Files (x86)\LaunchBarCommander\Jims Main Dock.mcf$0D$0A"
Maybe you can make sense of it.