Building GD-2.46 against gd-2.0.35 and jpeg-8c gets rid of the errors I was concerned about.

Of course, then I get slugged with this GD-2.46 test suite bug, but I'm not concerned about that.
Now it's just a matter of trying to work out why my static x64 build of GD-2.46 has suddenly decided it has to be built against a dynamic zlib library, instead of the static one that was fine last week.

UPDATE: I didn't exactly work out why it kept wanting to build against a dynamic zlib library. Eventually I realised that I'd added quite a few extra directories to the msys shell's path during the course of the day - when I reduced the path to simply what was needed to build gd-2.0.35, the problem went away.

Cheers,
Rob