The PDF indexer is multi-threaded. Each thread produces an output file. The load process combines them into the objects that are actually archived. If the load is successful all of those intermediate files should be deleted. Is it possible that you have files that are failing and leaving these intermediate files on the system?
As an example, a small PDF file (184k), when running index only, produced these files:
MH_MartForms_176pg.pdf.ind
MH_MartForms_176pg.pdf.out.003
MH_MartForms_176pg.pdf.out.004
As an example, a small PDF file (184k), when running index only, produced these files:
MH_MartForms_176pg.pdf.ind
MH_MartForms_176pg.pdf.out.003
MH_MartForms_176pg.pdf.out.004