And those message schema categories are configured in the services and operations that use that SearchTable? And, just as importantly, have always been there? It's not going to index messages that don't have those assigned in the message object's properties.

Are the Cerner custom schemas shown in your SearchTable based on InterSystems-supplied schemas? Is it possible that you need to specify "fully qualified" paths to the values you wish to index, for example:

Class XXXX.HL7.RAD.SearchTable Extends EnsLib.HL7.SearchTable
{

XData SearchSpec [ XMLNamespace = "http://www.intersystems.com/EnsSearchTable" ]
{
<Items>
    <Item DocType="InteleRAD_2.5.1:ORU_R01" PropName="AccessionNo" >{PIDgrpgrp(1).ORCgrp(1).OBR:PlacerOrderNumber.EntityIdentifier}</Item>
    <Item DocType="2.5.1:ORU_R01" PropName="AccessionNo" >{PIDgrpgrp(1).ORCgrp(1).OBR:PlacerOrderNumber.EntityIdentifier}</Item>
    <Item DocType="2.5.1:ORM_O01" PropName="AccessionNo" >{PIDgrpgrp(1).ORCgrp(1).OBR:PlacerOrderNumber.EntityIdentifier}</Item>
</Items>
}

What account is IRIS running under? Check Windows Task Manager | Details | User name column for the irisdb.exe task. It's that account's permissions that you're likely having issues with.