I am new to muCommander. Congratulations for the great job!
This is a low importance (rather estathical) observation:
I found that although using "-p path-to-preferences" commandline option works as expected, at exiting muC it just create an empty folder with the default name. The only special circumstance could be the fact that I put the new folder in the same subfolder it should have been created in (in my case the installation folder), but with a different name (./muco). I did use version 0.8.3 for Windows (XP SP3).