I had the same issue with a remote site that I could not keep all the computers in an online status. This drove my ticketing system crazy because of outdated signatures, when the signatures were up to date but just not reporting the fact.
After numerous calls with Symantec support, I finally bit the bullet and installed a remote SEPM. Once I pushed the new Sylink file to each computer, there has been 100% online rate from those previously intermitent computers. Should have done that months ago.
I'm convinced it has something to do with the networking between the remote site and the local SEPMs. Maybe the heartbeat, etc. Since this was essentially a network fix and not a Symantec fix, the Symantec support folks won't be much help. There was nothing wrong with my Symantec installs.