Alpha, textures and wierd graphics glitches

One of the problems im facing is that after modelling in max and exporting to .egg (materials and textures -including alpha- handled in max) and then loading into my program I experience wier graphics glitches like below:

As you can see the objects (glass in this case) using alpha from max are obscured and hidden (sometimes they just disappear) incorrectly when another alpha-using model comes infront of it.
Since I am using two seperate texture files (bmps) for each map in max (opacity and diffuse) i think the problem might be fixed through combining the alpha channel and diffuse channel textures into one file (maybe panda will be able to recognize it better this way?) and then use setTransparency(1) (using it or not using it at present doesnt remove the glitches)

Is this a common problem?

Well, of course I can’t see your picture (you’d have to host it somewhere and then post a link to it), but from your description I’m guessing you might be experiencing this problem: