@craigr: This is very concerning, we had worked hard to try and get a fix for all those cases so I'm sorry you had to go through that. For what it's worth, if you ever have to do that in the future you can save your programs as .fxp files and they should load in the new version.
Still, we tried to be very careful about that specific case, where 2.1 projects saved by an earlier version of Sonar were being loaded by Z3TA+ 2.2.1 in Lexington...
I'm confident you did the upgrade process correctly, but just to make me feel better can you check the version number in Z3TA+ 2's about screen? You open it by clicking the logo in the top left corner, it should be 2.2.1.
Edit:
Also, was this project coming from 2.1? Or was it coming from 2.2, our previous recent release?