Without knowing what you are doing in the scene its hard to say if its the engine or your code (even if you didn’t change anything, maybe you do something wrong and the penalty for that is higher in the latest versions).
After a bunch of changing to the stable Alpha-4 and back to the latest SVN, the problem seems to have gone away… still not sure what was causing it… but I’m no longer seeing the FPS drop… I’ll let you know if I see it again (with hopefully more useful information)