Document layout changes when creating PDF

We have the problem of the layout/formatting of documents changing whenever we try to print to PDF from, for instance MS-Word.
We open a large document of lets say 100 pages in total, then when we choose PRINT and now select ADOBE PDF instead of the default Windows printer, then the document layout/formatting changes and now suddenly htere are only 95 pages.
It is aboviusly some font setting problem, but we have not been able to find a soultion ourselves. This issue also prevents us from using "create from multiple files" as we cannot trust the final layout (page numberring end up wrong in PDF file)
Any input will be appreaciated.

Thx for the input. I am aware of the suggested workaround, but I was looking for at more "permanent" solution, as we need to combine 40-50 files for each job (Word, Excel...and more) and therefore we are trying to avoid having to go through all documents each time we need to convert to PDF.
Currently we are :
opening each document individually
then selecting ADOBE PDF printer
then checking document formatting/layout
then printing to PDF.
finally combining the 40-50 PDF's to one PDF
This we have to do as we cannot trust the formatting/layout.
It is off course undesirable when we know we can combine Word, Excel files to one PDF in one "go" without having to open the individual docs. at first.
Surely, it must be some printer driver setup issue (using printer fonts, enabling/disabling bitmap fonts, use truetypes....etc)? we just can't find the recipe for this ourselves.

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