Polarizing filters typically work fine with water or glass but often fail completely when encountering the Plexiglas used in aquariums, zoos and museums. Several years ago I bought a very expensive polarizing filter, IIRC it was B+W, that did nothing to reduce reflections from Plexiglas. I was quite annoyed about this and sent an email to them. IIRC the response was that while glass is a coherent substance Plexiglas isn't coherent at all. Reflections occur from the outside, the inside and throughout the particles of Plexiglas so polarizing filters just don't work very good. Mine reduced the picture quality a bit so I took it off.
So they gave you a long sciency answer basically saying, "Pexiglass. The stuff is just too dang thick".. lol. I tried a CPL a few times at various other places in the zoo where the lighting is better and like you I didn't find it to be all that effective. I've noticed my best bet is to stand back from the glass a bit and then look throught the viewfinder, if I spot some relections I need to move slightly or rotate a little until they arent there anymore, then wait for the shot I need. Not always perfect but the best solution I've come up with thus far.
Oh, Tree, forgot to mention I really like shot #2 - love the lighting on that one.