In nbif_v6_3_1_program_ltr() (and maybe other functions as well) you have
the following:

pcie_capability_read_word(adev->pdev, PCI_EXP_DEVCTL2, &devctl2);

if (adev->pdev->ltr_path == (devctl2 & PCI_EXP_DEVCTL2_LTR_EN))
        return;

if (adev->pdev->ltr_path)
        pcie_capability_set_word(adev->pdev, PCI_EXP_DEVCTL2, 
PCI_EXP_DEVCTL2_LTR_EN);
else
        pcie_capability_clear_word(adev->pdev, PCI_EXP_DEVCTL2, 
PCI_EXP_DEVCTL2_LTR_EN);

The comparison to (devctl2 & PCI_EXP_DEVCTL2_LTR_EN) looks wrong, as this 
expression
can only be 0 or 0x400. I think what you want is
if (adev->pdev->ltr_path == !!(devctl2 & PCI_EXP_DEVCTL2_LTR_EN))

In general I wonder whether the code part is needed and why pci_configure_ltr()
in PCI core isn't sufficient for you.

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