I've just update my stitcher to 5.6.2
No problem with stencils in 5.5 version
But ... what happend in 5.6.2 ??
Open a project, create a Stencil (delete outside - green mask), record project, re-open project and look at your mask : it becomes a delete inside stencil (yellow color).
 
I've just created 23 panoramas with masks (delete outside), ans used the batch function. All my stencils were transformed in delete outside stencils and I have a hole in all my panoramas !!!!
 
Anybody ?