Here’s a FrameMaker problem I had once on a 64-bit Windows machine. I don’t remember having it on my next Win7 machine, but I’ve seen it more than once.
The problem: the marker symbols were missing. These are the little “T” symbols you normally see when you insert a cross-reference or an index marker.
The solution: I did not have the fm5font.ttf font installed. I don’t know if the installer skipped it, or I did an install when I was supposed to upgrade, or I was just holding it wrong.
You can find this font in C:\Program Files (x86)\Adobe\AdobeFrameMaker10\fminit. Double-click it to install, then reboot.