RPE 700 DOORS Module Strange Behaviour Skipping Artifacts

I am having very strange problems with RPE 700 publishing large modules.

The general issue is that a about 10% of the artifacts (maybe 60 out of 600 - a mixture of text and headings) randomly get skipped as if they do not exist. The skipped objects then appear at the end of the document. As if the module had been published a second time sequentially and all the missed artifacts are picked up the 2nd time round.

If I repeat the publishing run then I get the identical output each  time with identical errors.

If I copy the module (duplicating all artifacts) and publish the copy then the error switches to different, seemingly random, artifacts. So in Copy2 a different 60 or so artifacts will get skipped and get published at the end in a second pass.

If I delete the 2nd half of the module so it is only half the size then the artifacts that were getting skipped in the first half (and shifted to the end) no longer get skipped but are now picked up and published in the correct position.

The template is very simple. Just publishes headings and text and applies heading styles to headings.

If I publish the module using the built in publish option:- Generate Report for Artifact>Print Module Book

...then the contents are published in the correct order. But I need to use a custom template to get the correctly styled output.