More info on the BOE issues,
With a suggestion from a co-worker I saved off all the sub reports and then tried (as a test) creating a different main report where the sub-reports are linked to the file of the sub-report and then posted them to a directory on the BOE server. The report functions the same.
I then viewed the sub-report by itself and the report ran without error and returning correct results. Where when running the main report returns "0" (Nulls). This technically is the same as the original issue ( the command string that was inserted into the server tells it to ignore the errors).