I think a lot of the difference comes from how the exhaust is handled as well as how good the intake air quality is. Other things to look at would be the weather conditions between different shops.

I've found that our dyno over corrects on the correction factor so if I'm trying to do A-B testing I have to confine myself to testing days where the weather is the same. I usually only test if the correction factor is close to 1.00 since the bigger correction factors don't seem to be accurate.

I'm not sure if there is any difference in power between the different brands of dynos. Acceleration rate and inertia factor and stuff like that can make some small differences but I think exhaust is probably the biggest issue most shops have.