I'd say the fan power supply on the smoke unit is suspect. I'll bet the capacitor may have actually fallen out, I've lost count of how many of those I've seen.
The other reason it could stop the fan is the smoke polarity is reversed. If this is a new installation, and it's never worked, that's a possibility. If the frame ground is going to one of the outside pins on the 3-pin connector, then the smoke fan will only run with boost as you're reverse biasing the diode on the fan power supply without boost.