@David-TP I can DM you me ISP as it's gives away my location, there is a chance that my ISP is involved as they are actively connecting fiber in our county, but the timing for when issues started was the first work-day after I insalled the X55 routers and the fiber work has been ongoing for months. Also I'm a total amatuer with wireshark but I can collect some logs from that if it would be helpful in identifying root cause.

All of my skype issues do indeed disappear when I log off from my VPN. Unfortunately skype is only a mild annoyance, the inability to access internal web services was fairly debilitating, but I've also found I have issues performing SVN commits (software which is writing, probably via TCP or HTTP, but I'm not positive, to a database on a mapped network drive that requires my VPN to be enabled) which are frequently failing after a few minutes in a several minurte long process, and Windows file transfers seem to always fail at the discovery/init phase of the transfer.

Disconnecting and reconnecting my VPN connection seems to resolve some of the time-related issues, but I had to do an endrun around the VPN to access to copy a large-ish (70MB) file to the network. It's worth noting that my current internet connection is abysmally slow, clocking in at around 12mbit down and 756kbit up, it's never caused issues like this and I've been using it with the VPN for years.

 I should add that I did enable MAC cloning, and ensured it's the actual MAC used on my old router, my ISP has stated that it doesn't track mac's and that MAC cloning isn't necessary, but I followed through. I have also tried a few reboots of the routers, I can't say for sure if those helped for a while or just made me feel like I was doing something useful.