Both growth spurts and a change in activity level can cause phe tolerance to change. Not getting enough calories can also increase phe levels by making the body catabolic, but since you said he is getting approximately 2000 calories a day that probably isn't the issue.
Does he go to school/daycare or is he under the care of any adults other than you during the day? If so I would speak to his other caregivers to see if maybe some sort of mistake is being made on their part (i.e. not measuring his food properly, accidently giving him food he shouldn't have, and so on). Because teachers, lunch staff, etc do not live with PKU on a daily basis and have not had many years to learn about PKU like we have it can be very easy for them to make mistakes without even realizing it. When I started school my mom said that my levels increased for a while, and she later found out it was because the lunch staff was not measuring my foods properly.