Yup, tried that with different cat 5e and cat 6 cables. I rule out cable issues (within the wall) by testing using direct cable connection to the router.
Yes, I found that the adaptive QOS and AI Protection does affect the speed, but these were the exact same settings that I had in my previous location and speed was at 800+ mbps then. If I turn off all additional rules or protection settings, the speed back then was 900+ mbps.
However, in my current location, I am getting only half the usual speed. With all settings and protection off, it climbs to 600+ mbps only.
Factory reset the Asus router and try again.
Have you upgraded the Asus router FW recently? RT-AC86U is an excellent AC router but I would not be surprised that Asus FW upgrade quality issue may cause your issue.
Are you using Ethernet backhaul or Wireless backhaul or mixed?
Switch off the RT-AC88U and second RT-AC86U to check iif AImesh is causing the issue or not, especially the RT-AC88U may have bad FW version and cause the Ethernet backhaul to become wireless backhaul.