Most will advise on using glass baffles as silicone really does not stick to plexiglass.
I, however, have used plexiglass baffles in my glass tank with silicone without problems. I put a good silicone bead on each side(s) of the baffle where it comes in contact with the glass. I also rough up the edges of the plexiglass about 1/4" in with sandpaper for added adherance. Doing this, I have had no problems with baffles giving out or leaking. The trick is a tight fit to start with.
Hope this helps!