We have the same issue.
What I did notice is that for our 3560s, 2921s and VG224s, this is not an issue. Those show up with their correct neighbors. However, all of our 2960s and 4500's do not show their neighbors in the PI topology view (of course if a device where the topology works and one where it doesn't are connected, they will both show up by virtue of the working one).
CDP is of course working for those devices and the neighbors show up properly both in the CLI as well as the various views in PI itself that show devices neighbors.