Ok, some sort of light. My reading said that the atomics were generated by the compiler for you, and they are. It turns out that right now, on my dev system, TARGET_ARCH is blank, so nothing special builds i.e. no atomics.
I set -march in my code, but had trouble setting it in the juce build - apparently both are required. Unable to feel certain I could force Make to use an arch, I hacked the jucedemo makefile with:
DEPFLAGS += "-march=i486"
And got the demo to build again.
So, if nothing else, it looks like the juce makefiles should detect a CPU of at least 486 - now they allow nothing (probably i386).
No-one else hitting this, really? Anyone know what/how I should set my default architecture? I'm on Arch Linux.