That's very strange, it should load all projects from the previous version fine... If you can, could you send me the plan file? If you feel uncomfortable doing so through this forum, you can email it to solarlune (at) gmail.com.
EDIT: And just to confirm, this happens when loading the plan manually from the menu, correct? Not when autoloading after starting MasterPlan?
EDIT 2: Also, what's your OS? Are you running it from the itch app, or separately?