I am seeing strange slicing behaviour when adding a raft with multiple processes. I have verified this on three different files, seen in the attachments. Here are the steps to recreate.
1) Import an STL with a hole
2) Create two processes, the first ending at the bottom of the hole (so that you force a solid layer at the bottom of the hole)
3) Slice and inspect the tool path at the transition layer, everything looks fine
4) Go back and add a raft, slice and inspect again
Assuming this isn't my computer only, you should see some strange tool paths: perimeters of the hole beginning below the transition point and/or solid layers or infill running through the hole. My best guess is that the raft throws off the process start/stop heights and the slicer isn't adjusting correctly. I have confirmed this also with a cube with a smaller cube on top and, again, perimeters for the upper cube can be seen starting below the transition point (picture 3).