I think there is a bug in PyMOL regarding the "set cartoon_transparency" setting. According to the PyMOL-Wiki, the arguments are:
set cartoon_transparency, value, selection
where the "value" ranges from 0.0-1.0 and the selection is optional. However, selections that are not entire objects does not seem to function properly as in other similar settings (e.g. set transparency). I tried the following test:
fetch 1bna hide all show cartoon set cartoon_transparency, 0.5, c. a #It should say "cartoon_transparency set for 280 atoms in object "1bna" ray
However, after ray tracing, no part of the object is shown as being transparent. Of course, when you leave out the optional "selection" then everything behaves as expected. I hope that this behaviour gets corrected for the next build.