@willhindson, I think it is possible that the GUI Git client (Git Tower) doesn’t use your local CLI version of Git and, instead, that it has this older version of git-lfs hard coded into it.
Are you using the most recent release of Git Tower? If not, it might be possible to resolve this by upgrading to a newer version of that software.
If upgrading doesn’t fix the issue, the workaround will be to make sure all initial pushes of any Git LFS media is first done in the CLI as this is using a git-lfs version which is new enough to be compatible and will set the content type correctly.
If you want to test a new version of Git Tower, please send me a PM/DM stating the day/time/timezone when you tested (it doesn’t have to be exact) and I’ll let you know what version git-lfs it reported when it connected.