I have been having weird ligature issues for some time on random jobs.
I have been having an issue with Indesign and PDF files
We are getting font character "Glyphs replacing other characters"
Specs of the machines
ID version=ID-CS5 ver 7.0.3
Acrobat Distiller version = 8.0
Fonts we have had this issue with
Sabon LT Std.
Garamond MT Regular
Fairfield LT STD
Palatino LT Std
Minion Pro Regular
Times New Roman PS
Adobe Garamond Pro Regular
Characters that have been causing the issues.
io, il, hn, hk, SY
The characters they are replaced with.
Ú Ÿ Õ Š Ỳ §
We run font cache cleaners such as Font Nuke, Font smasher and we even created our own from information found in other places where all the font cache's hide as well as suitcase's.
We tend to catch this issue in out PDF outputbut it does show up in the Indesign files. We have noticed that when we catch it in the Indesign file we can turn of ligatures in the Paragraph style and the characters go back to how they should display. But then the fi, fl, ffi, ffl, and Th ligatures are gone in the paragraph.
We process many jobs on a given day via 3 different machines that are setup to create PDF files. On total we do about 170 new jobs in a month this doesn't count revisions of the job and since August we have only discovered it in 11 jobs.
Other people are having similar problems but similar to our issue its not something one can replicate all the time.
Please see the following link to the adobe forums.
Link to the image of the issue on Adobe forums.