Hi ABraun,
Please note that the AOI BBOX definition it only used during the coregistration-interferogram computation on those scripts.
For the splitting, the IW is the parameter to consider during the splitting step. Was it defined in the project.conf file?
In addition,could you post the final xml which the scripts run? It might be called something like splitgraph2run.xml that should be found in the PROJECT/graphs/ folder.
With that info it should be easier to identify the issue.
Please let me know it this helped.