Disulfide bonds are indicated in PDB files by the presence of CONECT records containing the serial numbers of the bonded sulfur atoms. I'm imagining your PDB files are lacking these CONECT records. If Chimera had written these PDB files the CONECT records would be there, so you must be using some other tool to generate the PDB files.
Probably your simplest workaround (aside from using Chimera to generate the PDB files in the first place) is when you have such a PDB file open, use the command "sel :CYS@SG" to select all the cysteine sulfurs and the use the "Adjust Bonds" tab of the Build Structure tool to "Add reasonable bonds between selected atoms". You could then save a new PDB files so that you wouldn't have to do those steps over later.
--Eric