The user reconciling can be the only edit session within the version in question. The exception is if the target version is the DEFAULT�??you can reconcile against the DEFAULT even when other users are editing it. If you do not expect other connections and edit sessions to be leading to this behavior you could have hung connections within yourrepository ( check: process_information and locks tables) yet as this only occurs from "time to time" it may simply be another session conflicting.
Reconciling a version
When a session starts a reconcile, the shared locked is promoted to an exclusive lock, succeeding only if no other shared locks are present. Promoting the shared lock to exclusive ensures no other sessions are currently editing and no sessions can start editing while the reconcile proceeds. The lock is not released until the post operation or stop editing.
sdemon -o kill -p password@instance -s servname -i sde : oracle11g -N -t all