Hi Richard,
You may not be making font decisions, but your PDF is making those decisions. If you create a document in Word, for example, all of the fonts available on your system will be available to use in your document. You cannot use a font in any other program that is not resident on your current system. But a PDF may contain fonts that are not on your system, but also not embedded. In this case Acrobat tries to make a suitable font substitution.
It is possible to use full embedding, in which case the entire set of glyphs used in your font family is embedded in the file, but typically users apply subsetting. This means that only the actual glyphs used in the PDF itself will be embedded.
One can find out which fonts are in a PDF by clicking CMD + D, for document properties, then selecting the Fonts tab (Win is Ctrl + D). There it will tell you which fonts are being used and what the situation is wrt embedding.
Also worthwhile in the Doc Props dialog in the General tab and identifying the PDF Producer. Only Word and Excel from Microsoft can create those documents but there is quite a proliferation of applications these days that can create a PDF, not just from Adobe.
A couple of years ago a research scientist was quite upset that his 900 pp document was failing to convert to a digital print format using Preflight. We ran some tests and found out that (a) the producer was a typical text editor used in scientific research that (b) wasn't able to properly embed the fonts, which (c) themselves were quite rare anyway on not on his system. But on the surface it looked like Acrobat was failing somehow.
I will still pass your issue on as well. Might also be good if you went on the Brother website to see if anyone else is posting these problems and perhaps solutions.
Thanks
Mark