I thought (only 5 minutes casual googling) that the laser was controlled either by a TTL or PWM signal? But I'm struggling to find the spec of the PWM signal (frequency, and active level, 0%/100% reference pulse widths)

What are you driving the PWM from? (e.g. a PWM output from a BoB?) In which case there may be a general sensitivity to the PWM frequency (and you might need a mini interface to take PWM of one frequency, and re-present that at another). That's all do-able and a cheap ardi (that you already have) could be brought to bear to achieve that.

Any documentation with the laser?