I'm using the latest build of the mod and just completed my first tower mission in my starting region. Upon completion, all non-Psi members of my squad where reset back to Squaddie level. Beyond loading up the final save to finish the mission again, I've taken no trouble shooting steps because quite honestly I wouldn't even begin to know how to troubleshoot this.
I have another problem that may or may not be related. Since installing this mod I'm getting significant perforance issues with frequent crashing in the cut scene of the Skyranger returning to the Avenger, requiring me to use the Task Manager to close the game. One such crash occured before the level reset occured. I've tried uninstalling and reinstalling the mod but it makes no difference. With it I get performance issues I never get in the vanilla game.
Level reset
Re: Level reset
Did you follow the troubleshooting steps for regenerating .ini files? That may solve your performance issues. As far as the rank reset goes, this is the very first time I've ever heard that happening. What other mods are you using, if any? Both of these may be a mod conflict issue.