You can delete the queues directly from the Oracle level using sqlplus:

1) Shutdown the Method Server
2) Log into sqlplus as the windchill user:
       sqlplus windchill/windchill@wind
3) Delete the non-executing entries in the publishing queues using:
       delete from queueentry where targetmethod='doPublishJob' and codec5 != 'EXECUTING'; 
4) Delete the entries in the processing queue using:
       delete from queueentry where targetmethod='queuePublishJob';
5) Confirm the entries left in the queueentry and the processingqueue tables using:
       select pq.name,codec5, count(qe.ida2a2) from queueentry qe, processingqueue pq where pq.ida2a2=qe.IDA3A5 group by pq.name, codec5;
6) Commit all changes using:
       commit;
7) Restart the Method Server