I too am expericing this.
just to explain a little in how I got this my process is
I start with a PDF that I need to grab data from, I open in Illustraitor and copy the content I need in to InDesign. it all seems to work even in preview, but when i export into PDF sometimes some of the characters turn into the boxes
Please start a new thread rather than tacking onto this one which is now nearly 4 years old. When you do, please tell us the operatiing system, and the version of InDesign, as well as the patch level, that you are using.