This is interesting, but I am not sure I recognize what is the question(?) So I will first test my understanding.
You are running an unspecified Oracle version on an HP ML370 G3 server with Win 2k. What is the Oracle version?
You have both an active database and a passive database, but the replication mechanism is unspecified. Is this using Oracle Data Guard? a physical standby? a logical standby? Golden Gate or some other replication mechanism?
An example of a problem I have seen with Logical Standby is that if an ID is created first on the standby, and then the same ID is created on the Primary, then the SQL to recreate the ID will get to the standby and then fail to apply, and then replication is dead for a while until we skip the statement that fails to apply, and then after having skipped it there may be much CPU time consumed to apply other pending SQL. This isn't exactly the scenario you describe, but in some form it sounds like you may have a similar experience... it is necessary to take care in how one administers Data Guard.