Do you see the following exception from APS(with search service) logs:
Exception - Could not open file: <installdir>\Filestore\Input\<folder_name>\<filename>.gen
If so, please check SAP KB 2096653 - Indexing blocked due to inconsistent delta indexes and surrogates on http://service.sap.com/sap/support/notes/2096653 and the fix is included in BI4.1 SP06 and above.
Regards,
Jin-Chong