I'm certainly not an expert on CONECT in .pdb, but in my experience CONECT has exactly that problem. When we introduced Rasmol as a viewer into our CaGe program, I looked into "set connect" as a possible means of making Rasmol follow the connection information in the file exactly. I remember reading in some manual and deciding that "set connect" would not do that for me. Colleagues that were using Rasmol for a long time (in the previous version of CaGe) always said there was no way of "taming" Rasmol. As a result, we only run Rasmol after displaying a warning to the user. When people on the list wrote about their interpretation of "set connect", it seemed like the meaning I would have wanted for the command, but I didn't take the time to check up on this, so I didn't comment.
If you're after connectivity, I guess you'll have to investigate precisely what "set connect" does and does not do. My idea is that whatever you do with "set connect", there is always some chemical interpretation of the data taking place, and I gave up on trying to understand or influence that algorithm. That's one of two reasons why I want Jmol's CML reader to accept a "MathGraph" molecule convention. (The other reason was that I can pass CML data in an applet parameter, whereas PDB data could only be passed through a file in Jmol 0.6.1.)
Sebastian
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