Controlling printing applications

I have an application that prints reports and sends then as faxes. All
this is done under program control. The report is printed to a Word Doc
or a PDF and then that document is sent off to MS Fax.

This is all done with FaxComEx...

When sending the document to the fax, the associated application is
brought up to actually print the document.

This is a problem in that the associated application just pops up and
then (if I am lucky) disappears. This is driving my users to drink.

Is there any way to fax PDFs and DOC files (or, worse comes to worse,
just PDFs) without having an application popup to my user? I don't care
if an app runs in the background without it being visible to the user,
it's having an application popup on them that is the problem.

ALTERNATIVE #2 - Is there a file format that MS Fax can handle natively
without an associated application?

TIA
.

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