Why are my cookies undercooked in commercial oven?
I think there are a couple things to troubleshoot here.


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.
Could the oven be steam-injection? that could cause some problems with done-ness. 
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).