Hi there,
There are few things that I would like to verify --
is the client machine and the see server in same domain??
When you try registering a user on the client machine -- what is the error message you are getting ???
Which version of see you are using ??
the client machine that is not checking in which OS is installed ???
If you go to C:\Program Files\Symantec\Symantec Endpoint Encryption Clients\TechLogs on the client machines -- check what error message is coming up ???
make sure that EAFRcliManager should be automatic and started on these machines ???
When you try opening See config console or the see manager on the server -- is there any error message that comes up ???
the machines that are not checking in -- was it a fresh deployment of see on them or an upgrade ???
Also there is no need for you to uninstall see server and start from scratch -- I am sure that there is something not correct specific to few machines because of which they are not checking in ......