I haven't seen this issue, and I use skirmish for quick tests of builds.
Then again, I use the default "multiplayer_initial" for the equipment list when I start a skirmish game.
This probably isn't the answer to your problem, but as a long shot: Have you tried deleting the config files in your application data folder between revisions? More than half the time when I update and re-compile everything that solves various issues for me.