I have the same issue that you guys are having.
I have 1500 Clients and 95% of them are version 12.1 RU1 and so is my SEPM
Every day I am getting notifications that 30-40 clients are not updating. If I restart the smc service and wait a while it finaly updates.
My SEPM is setup to Push mode with a 5minute heartbeat with any client on the LAN and Push mode with a 30minute heartbeat with any client across the WAN.
All the clients on the WAN are using GUP's per subnet and everything on the LAN is talking directly to the SEPM.
One thing I have noticed however is that 90% of the clients that I visit to restart the smc service on they are logged out and the PC is sitting at the login screen. From there I dont bother logging in and I just give it a restart (pretty much same thing). And then again the other 10% are logged in.
So not to sure what is happening here but this didnt happen on 11.6 from memory.