Clean room issues

Hello i am new to the website and i am eager to learn. I have recently had a clean room built and installed in a location. We have a clean room and a ante room. We have two Magnehelic guages. One outside the ante room which reads the pressure in it and one in the ante room which monitors the pressure in the clean room. We have the system set up that the hepa filters run all the time regardless of if the compressor is running or not. When the compressor has either cycled of or not running i am reading .04 on each guage which is within the guidelines. However once the compressor kicks on the pressure in the clean room rises to .11 and the ante room stays at .04. I spoke with the company who is going to be accrediting are clean room and they said it is not suppose to operate this way. The pressure should remain close to the same regardless of if the compressor is on or off. They also said in its current state it would not be able to pass accreditation . I will be contacting the HVAC person to work on this but does anybody here have any idea of what might be going on. Thanks in advance. Also one thing i noticed was on the door going into the ante room about a inch and a half was removed from it to allow some of the pressure to escape from it and keep its pressure down. The clean room door has not had any inches removed from it and scales the full size of the doorway. Could this be the issue ?