I have same issue & I’m just using After effect then importing it into Encore. it only does it with Blue-ray loop point is not seamless like it is with DVD. I saved a disk image thing it might be my blue-ray play but it does same thing on my computer with a image file mounted.I heard its in with the programming for Blue-ray & cant be fixed unless the programmers fix the issue with an update. but there is a program called BDedit that you can fix it by saving project as a folder & importing it into BDedit & after burning it using another burning software.