I have analyzed a little bit the problem. The bug should be related to
the module acpiphp because the problem persists also in the 3.5 ubuntu
package if this module is not loaded. then I have downloaded the ubuntu
pathes applied by ubuntu and I have found a part that is related to this
module:

--- linux-3.5.0.orig/drivers/pci/hotplug/acpiphp_glue.c
+++ linux-3.5.0/drivers/pci/hotplug/acpiphp_glue.c
@@ -132,6 +132,15 @@
        if (!acpi_pci_check_ejectable(pbus, handle) && !is_dock_device(handle))
                return AE_OK;
 
+       status = acpi_evaluate_integer(handle, "_ADR", NULL, &adr);
+       if (ACPI_FAILURE(status)) {
+               warn("can't evaluate _ADR (%#x)\n", status);
+               return AE_OK;
+       }
+
+       device = (adr >> 16) & 0xffff;
+       function = adr & 0xffff;
+
        pdev = pbus->self;
        if (pdev && pci_is_pcie(pdev)) {
                tmp = acpi_find_root_bridge_handle(pdev);
@@ -144,10 +153,6 @@
                }
        }
 
-       acpi_evaluate_integer(handle, "_ADR", NULL, &adr);
-       device = (adr >> 16) & 0xffff;
-       function = adr & 0xffff;
-
        newfunc = kzalloc(sizeof(struct acpiphp_func), GFP_KERNEL);
        if (!newfunc)
                return AE_NO_MEMORY;


The name of the module is mentioned in other parts  in the patch so I
think that this code is not enough. Anyway I think it could be very
helpful for you.

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https://bugs.launchpad.net/bugs/1159418

Title:
  plug and play with thunderbolt devices was working with 3.5 but is
  still not working with 3.8

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