Module version mismatch with headless browser and desktop Node

I'm getting a "Module version mismatch error" when I try to use a headless browser with a desktop Node shell. I've tried Zombiejs and Phantomjs with both nw.js and atom-shell; in both cases as soon as the headless browser comes into play the application crashes with a module mismatch error.

Here's the error with Phantomjs and atom-shell:

Uncaught Exception:
Error: Module version mismatch. Expected 41, got 14.
    at Error (native)
    at Object.module.(anonymous function) (ATOM_SHELL_ASAR.js:118:20)
    at Object.module.(anonymous function) [as .node] (ATOM_SHELL_ASAR.js:118:20)
    at Module.load (module.js:370:32)
    at Function.Module._load (module.js:325:12)
    at Module.require (module.js:380:17)
    at require (module.js:399:17)
    at bindings (/Users/Ajay/Projects/atom-shell/node_modules/phantom/node_modules/dnode/node_modules/weak/node_modules/bindings/bindings.js:76:44)
    at Object.<anonymous> (/Users/Ajay/Projects/atom-shell/node_modules/phantom/node_modules/dnode/node_modules/weak/lib/weak.js:7:35)
    at Module._compile (module.js:475:26)

Any idea what's causing the error?