The mannual scatter-gather of BQSR output differs from gatk-queue BQSR scatter-gather run

Hi,
I tried to run BQSR 32 times parrallely each with a contig I specified using -L option, there are no spaces between the contigs, then I gathered the reports with GatherBqsrReports tool. The output seems have large difference with the default gatk-queue scatter-gather BQSR run. I dont know why is this, could anybody explain that to me or give me some advice? thanks so much