The Personas 2 to 3 migration process doesn't guarantee to produce Personas 3 flavours that work fully. You have to test each one and will likely need to apply manual changes - to the layout, or scripting, or maybe both - to get them working properly. How much manual work is required will depend on the flavours themselves. Some may not require any, some quite a bit.
You're now going to have to debug your flavours! Start by reading this wiki page - Debugging options in SAP Screen Personas 3.0 - to see how to go about that.
Steve.