Why are my cookies undercooked in commercial oven?

I think there are a couple things to troubleshoot here.

1. Check that the oven is working. you can buy an in oven thermometer to verify that you are getting accurate readings. seems you have done this already.
2. Could the oven be steam-injection? that could cause some problems with done-ness.
3. Maybe some other part of your process is different now that you are working in an commercial kitchen. Note act 14 in this episode, small things you change can have huge ramifications (in this case not letting the meat rest for a short time lead to a drastic reduction in flavor and color).

There's something else that you may need to test -- how many pans you have in the oven at one time.

Most home ovens only have two racks, so you're never cooking more than two sheets of cookies at a time. This means that they'll have radiant heat from either the top of bottom. Some cookie recipes are so sensitive to radiant heat that they'll specifically mention that you should only cook one sheet of cookies at a time.

And as you say that the outside of the cookies is done before the inside, this typically means that you need to turn down the temperature slightly, but increase the cooking time. You may want to just adjust your recipe in this way, so you can make proper use of the commercial oven, rather than trying to figure out what to modify to make the commercial oven behave like your home oven.