Checking IRQ routing table consistency... Inconsistent IRQ routing table size (0x90/0x70)
That looks bad, not sure where it came from.
You didn't show us all boot messages, only the messages at your default kernel log level. Try "dmesg -s999999".
Anyway, this looks related:
0xe00, /* IRQs devoted exclusively to PCI usage */
and sure enough, the interrupts that got assigned were 9, 10, 11, 9 (in the order of your irq_table). Dunno why no non-exclusively-PCI IRQs were used by Linux.
Segher