I noticed that the libretro dlls did not get updated with RetroArch. Attempting to update them via Phoenix tells me they have already been downloaded and offers to use them instead.
Is there a process to update libretro dll files? If not, maybe if there is a repository of compiled ones somewhere a simple app could be written to check versions and update them.
Also, the remote part of Phoenix or can it be used when launching from the command line as well?
EDIT: The update included the new built-in support for DirectX, I was still configured to use the external DLL for it. Changing this resolved the issue. I am still curious about the other questions though. Edited the above to remove parts about the error, though below I will explain in case someone else has the same issue.
I had a code 1 error, RetroArch would fail to launch, this was because the video settings were configured to use an external DirectX driver rather than the new internal.