This may be outside of your control as the issue could be with the originator of the original PDF file. Arial MT is a PostScript Type 1 font that is installed somewhere along your workflow. I believe PDFs will attempt to convert this to a TrueType font, or not depending on how the app creating the PDF is configured.
Is it possible that a number of people are creating invoices you receive? If so, it might explain why a small percentage fail. Can you trace who has created each PDF as this may be your best bet.
Thanks for your response and sorry for the delay in getting back.
The invoices are coming from external companies, so we don't have any control over how they are generated.
So looks like we just have to live with this problem.
Should I find a solution, I will add it here.
If you are interested, we could process the PDFs with DynaPDF and replace fonts / rebuild the file.
With MBS Plugin.
e.g. we used our optimize command before to fix issues in FM generated PDFs.