When you are printing direct from inside FL, you are printing are raw outlines, not a font per se. When you generate a font, install it and create a document in InDesign, you get the outlines as handled by the font layout engine and, most likely, with hinting applied.
Hello,
Has somebody encountered problems when printing to PDF from FL? I'm trying to generate font samples, but the glyphs are distorted!

Take a look at the screen capture. There are some strokes noticeable darker than others... strangely, when printing to PDF from InDesign everything seems to be OK.
What the problem could be?