For Windows 2022 custom AMI,

ec2 instances created using custom AMI were not running userdata.

You need to run sysprep shutdown command while creating AMI. So when you create ec2 instance using this custom AMI, it will run userdata.

"& 'C:\Program Files\Amazon\EC2Launch\EC2Launch.exe' sysprep --shutdown"

I followed this references for sysprep command since I used Packer to create AMI. https://gonzalo.f-v.es/blog/2022-10-14-windows-2022-eks/