I have a current setup where we have two lan subnets. 192.168.16.x assigned to LAN port 2 and 10.0.0.x on LAN port 1. LAN port 2 is also a tagged VLAN 20. This was to provide the enterprise wifi system with a guest access on the 192 subnet and also to prevent cross traffic over the lans (inter route is unchecked). Yesterday I got a call that some users on a particular switch were no longer getting access to servers/shares etc and on investigation I found that I was able to ping from the 10 subnet to the 192 subnet, this inturn caused a routing loop which was what the users were experiencing. I have since removed the second lan connection from the switch (the switch was tagged VLAN 20 also with no membership on that port to the default VLAN).
I have tried removing the config and doing it again but still get the same issue, anyone had experience with this? It worked well for months and there were no config changes made at the time to change it

Have you checked out - https://www.draytek.com/support/knowledge-base/4912#linux

Also have you done,.

Reboot the router
Check for firmware update

Yes to all.
I have also had the Draytek support look at it and the config was good, they are currently testing it I believe but have not had a response for a couple of days now.