Hello,
I am using 3.5.5, windows 7 64bit
I have a transparent layer and I drew a circle. I then copied and pasted the circle in the same layer expecting to see two overlapping circles (ie a Venn diagram). However the bits that should have been transparent were erasing the first circle. However if I pasted the circle into a new transparent layer then it worked as expected. Nb if there was a picture in a layer below, then the first circle would get erased but you could still see the picture below (in other words it was overlapping the first circle with a "transparent colour").
I have done an attachment that shows what happens if you paste into the same layer and into a different layer (tried to paste the pictures in the message but they went funny).