Hi Qamar,
have you tried using "MSBATCH.BAT" - our batch process command line utility - to process you batch process job? You can find information on how to use it in Microstation's help file but its syntax is the following:
msbatch batchprocess <batch_process_job_file_specification>
For example: msbatch batchprocess C:\ProgramData\Bentley\MicroStation V8i (SELECTseries)\WorkSpace\Projects\Examples\General\my_batch_process.bprc
Can you execute a standard check correctly using the Bacth Process Utility and the same bprc file?