Actually this wasn't a save file bug buta real bug, I finally found and understand the problem after taking a look at your save file again.
The script I use to save the party order only saves the active party order in battle leading to this mess up order sometimes when having more than three members.
I am preparing a new version right now, in that it should be fixed.
Tell me after you had time to try it.
And tahnksa lot for finding it!