I'm trying to print a model with 2 regions, with the auto-generated raft + supports. The supports on the 2nd level don't generate a raft under them and also it seems that after printing the raft the print head moves down to the 0 level to print the supports which scrapes and destroys the raft it just printed.
These issues should now be resolved with the new changes in Version 4.0. This version included a completely new raft design with improved placement and printing.