Something similar happened to me a while ago but with databases rather than servers.  In that case I was using SQL 2000 EM to take SQL 7 databases offline.  Somehow, SQL server managed to put a data value that was bigger than could be supported by the data type in the sysdatabases table.  I recall that it was cmptlevel, which is a tinyint; selecting * from sysdatabases it returned an error at the row that had the doggy data value.  Changed this value and all the databases reappeared in EM.  It may be that there is something similar going on with your disappearing servers.