I know this may be an odd, and possible stupid question, but I don't know how many agents you're referring to or where they are located. If the agents are at a client location, have you been able to narrow it down to any certain locations? The reason I ask is that it could always be ISP related at your client's site. We've had instance in the past where a number of agents have gone offline repeatedly at certain times during the evening at numerous clients. At first we assumed it was Kaseya related. Then after further investigation we found that all of the clients were using the same ISP. After discussing it extensively with the ISP, we worked with them to troubleshoot down an issue on their end that was causing outages at roughly the same time each night.
Of course if all the agents are on premise with the KServer, then that pretty rules out that as a possibility.