I (naively) went through pci/pm git log and found the following was applied on 4.7-rc2 (i.e. prior to 4.7 release): commit 006d44e49a259b39947366728d65a873a19aadc0 Author: Mika Westerberg <mika.westerberg@xxxxxxxxxxxxxxx> Date: Thu Jun 2 11:17:15 2016 +0300 PCI: Add runtime PM support for PCIe ports From reading the commit log it seems to me like it could be it. ath10k tries to wake up the device during probing before it starts talking to it and it does so through MMIO/PCI config space. If it's not mapped properly then driver will not be able to wake it up and will timeout waiting for it. Can you try cherry-picking it into your 4.4.24 and see if it helps?
Thanks for the help! Until now I did not compile a kernel for the board. I will give it a try and come back with the results ... Best regards, Matthias