Yes, I'd suggest that you add "vertical" ground jumpers in your patchbay alongside the normals. Generally, patchbays should be wired so that electrically, they "look" the same to the gear as a direct cable would. So carry the ground through the patchbay. Think of it as a continuous piece of wire (that happens to have a couple of extra connectors in line).
If things worked before with your old patchbay, which sounds like it carried the grounds, they'll probably work again if you add the jumpers to your new bay.
As for telescoping grounds on inputs to the gear, first get back to the quiet situation you had before, with the old bay. Try monitoring one item with a lot of gain and see if you hear any background noise. If you do, you might try cutting the shield on its input, as an experiment, to see if there's any improvement. But keep in mind the "if it works, don't fix it" credo, and don't make a whole bunch of changes unless you are 100% sure there is a problem, and that the changes really help.