Seen with blender 2.54 svn r32610, 64bit linux
running and built under kubuntu 10.04 64bit
geforce gtx 460 with nvidia driver 256.53

The z-combine node in the compositor does not take any alpha values into account, thus making this node unusable when dealing with transparent objects.
It can be worked around by using the zmask ( or All-Z) feature and using alpha over, but i think this should also be handled by the z-combine node.

Since the source code doesn't seem to have changed since 2.49, this is also true for the current stable branch.

It may be a deliberate decision to ignore the alpha values, but nonetheless I have included a patch which corrects the problem (at least with the examples done by me so far)

See the attached blend file for an example. It has 3 planes. The top-front and far-back plane are rendered on one layer with the front plane having an alpha mapped texture applied. On a second layer the middle plane is rendered, also with an alpha mapped texture applied.
In the compositor these two layers are composited using the z-combine node. The behaviour with the current svn shows that the alpha values are ignored.