You already RMA'd the MX75 and tried a MX67 and the problem persists. I can't imagine trying yet another MX67 is going to change the results. I also see Support changed the MTU and MSS clamping for you. Any difference with those tweaks in place? I took a look at your MX and other than small blips on the loss chart for the WAN link over time I don't see anything that catches my eye in your config. You mentioned running ping tests on a server. What was the destination? The MX LAN IP, another LAN IP, internet IP? Also, do you see the same loss when pinging from non server clients or the switch (if it's a managed switch that allows for it)? Also, what is the complete topology of the site? I see LAN ports 4, 7, 8, 9 are active. What do they connect to?
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