On the 6509s, which dont show the VLANs, check in the .cfg files and see if the targets are there but commented out. Similarly, on the 4507s, see if the ports are there but commented out. If they are, there should be a preceeding comment to tell you *why* they are commented out.
On some switches, the SNMP returns non-unique port names and you have to use port numbers. When you call cfgmaker, pass different ifref parameters and see if this helps.
Finally, if you get it all working and showing all the ports, you can use the routers2 special functions to group the VLAN and port graphs, if you want. You will need to edit the .cfg file and either add routers.cgi*Summary definitions (to make special summary pages with multiple graphs on one page) or routers.cgi*Graph definitions (to make userdefined graphs with multiple lines on one graph). If you do this, you shoul make sure that you dont overwrite the file in the future with cfgmaker.
UNIX Systems, ITSS, University of Auckland, NZ
Woe unto them that rise up early in the morning... -- Isaiah 5:11