As long as your Consolidation Algorithm Type is set to anything but Custom (in Cube Properties), I would expect Accounts of any type to participate in IC elimination - assuming they have been marked with "Is IC Account" true, with a plug account defined, and all the relevant matching filters on the Workflow Profile. Note that discrepancies can arise from imprecise translations, you might get some detail from your IC Matching report in Workflow.
If your Consolidation Algorithm Type is Custom, though, it's all due to the Business Rules that have been developed; in which case you probably need to speak to whoever wrote them.
