Since your EC2 server(s) having higher CPU, you might have installed some memory consuming apps. such as Antivirus, Window Update Application.
Or it could be due to some process running or consuming lot of memory putting all server resources to consume leading to performance loss.
I would recommend you to check from Task Manager, at the moment when site goes abnormal or slow, which process is taking lot of memory at that moment. I can bet that either it can be some virus infection or antivirus trying to update itself and interconnected client pc.
Let us know back the action result.