I think that's an old program and perhaps it doesn't work as it should these days.
What I suggest you do is, if you aren't already, use GCFScape to browse the contents of your map's pak lump, so you can see what is being packed in. Then use CompilePalX to pack your custom content. Its auto packer tool is currently the best you can get, as it picks up loads of different types of stuff. If you prefer, you can configure it to create a text list of assets to pack, and use that list with bspzip directly.
CPX is a batch compile tool and is usually used for all compile steps. But you can deselect the VBSP, VVIS and VRAD steps to avoid compiling a map again if you just want to pack.
Note that repacking a map (BSPZIP compress) should be the last thing you do prior to distribution, and that it's not possible to edit a map's pak lump afterwards without first decompressing it.