Could you be a little more clear, the 2 seem to be opposite issues....on one hand nothing is transparent, on the other you have clipping issues....what image types are you using in both cases.

do the plants use a tga with a mask(32bit)
the car and the building what are they using?

Everybody Poops.
here are some tutorials I made.
http://www.acknexturk.com/blender/