If it does occur with "FI", then there's something seriously wrong with the font or the printer driver! Perhaps it's "FI" in small caps only? (Now that would indicate a bad font -- not quite totally unheard of, but still a very small chance)..
The sequence "fi" commonly gets replaced by a single character glyph -- the "fi" ligature. If it does look allright on screen (surely you should've noticed if it doesn't), but appears wrong in a PDF or on your printer, you should check if your fonts are downloaded correctly to either PDF or printer.
Known culprits are wrongly subsetted fonts (do you have placed PDFs in your ID document?), weird settings in the Export or Print dialog (change the subset options and see if something changes), or in the Windows printer setup (assert all fonts are downloaded, rather than "replaced by printer font").
Make a single page document, containing text with common ligatures: "Difficult flimflam afflicting floundering files" (or something to that effect). Export the document to a PDF from InDesign and check. Print to a PostScript file, distill it and check.