In ShareScan 5.4 with hotfix 4007, when using Smart Forms Extender, single page documents are processed correctly. However, when batching is enabled, documents are not split, no output files are created, nor is anything stored in the reject folder.
On theSmart Forms Extender's Configuration (Admin Console) UI, in the Image Cleanup section turn the option "Modify Output Images" ON and select a cleanup operation. It is recommended to use either Deskew or AutoRotate as a cleanup operation
This is planned to be addressed in a future software update.