I use an AMD R9 Nano graphics card, along with AMD's Radeon Settings program and I noticed that in addition to Windows update installing things for windows ...it will also update apps it finds in the MS/Windows store.
I went to Windows 10 Control Panel > System > Settings and changed this from Yes to No.
This stopped my AMD Radeon Settings / program from getting automatically updated, which would also change/revert/update my graphics card settings, similar to the freezes/crashes/etc that you have been experiencing.
I'm sure that auto-updates to AMD Radeon Settings is great for modern games, but for FFXI, once I get it working, I stop updating graphics card settings/drivers.