Ok, have had a response from iManage in regards to this, and there is definitely an issue with the current 9.3 Filesite client and Office 2016/W10 combination.
There are multiple issues, which is why its been so difficult to work out.
Issue 1: Office 2016 renders using something called Airspace, which is different to Office 2010. The issue is it requires a LOT more memory and transactions in order to work. (https://blogs.technet.microsoft.com/outlooking/2017/09/06/32-bit-outlook-interface-elements-unexpect...). Higher resolution screens will often freeze, or show up white/black boxes, or just not refresh properly. The answer to this is to move to Office x64, which addresses the memory issue.
Issue 2: Instability after Windows 10 1507. I actually have a client that had a WSUS issue on their machine, so they never got off the original W10 build. They also never had any iManage problems. It seems that anything beyond vanilla 1507 causes general instability, freezing, not responding etc.....
So at the moment, if you are stuck in a W10 environment, the recommendation is to move to an x64 environment. I have also personally tested Desksite, which resolved all stability issues.