Stitch lines that appears in artwork is caused by flattened transparency during PDF/X-1a export, not the compression setting.
It sounds as though your document contains many images with transparency applied, and perhaps multiple elements that are layered over top of one another with transparent effects. If that is the cause, exporting with any setting that retains transparency, you may experience errors or incorrect image composition.
The work around suggestion would be to export smaller sections. And if you need to supply a complete (all pages) PDF, use Acrobat to merge multiple PDFs.
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