I have discovered a curious issue on the iMX6SX with the Linux 4.14 code base using PCIe on the A9 while the M4 processor is booted.
I have found that I can build a working version of Linux 4.14.78 which will boot reliably, and allows me to use the PCI bus over PCIe.
However, if I load and boot the M4 processor (e.g. I build and load one of the M4 processor example programs) from uboot 2018-03, and then boot the exact same Linux, it hangs when trying to configure the PCIe device. It freezes on a read instruction when it first tries to access the PCI configuration space. It appears to be something to do with the Resource Domain Controller (RDC).