Here's another data point: I found some PDFs under my Documents folder that weren't showing up in AMF. I found that simply opening one up in Acrobat Reader would cause it to show up in AMF (I didn't have to change and re-save the PDF).
I did notice that if I selected multiple PDFs at once and opened them all at the same time, some of them would then appear in AMF, while others wouldn't. But opening up a single PDF by itself would always add it to the files shown in AMF (as long as the PDF was somewhere under my User folder - if I first copied the PDF to a second hard drive that's not under my User folder and *then* opened it, it still wouldn't show up in AMF.)
In short, here's what I've discovered so far:
1) AMF doesn't seem to index anything that's not somewhere under my User folder.
2) Not everything under my User folder shows up in AMF, but if I open a "missing" file that's under my User folder, it will then show up in AMF. (Except for pictures and songs - see #3)
3) AMF doesn't index anything that's in my iPhoto or iTunes libraries (even after opening a picture in iPhoto or playing a song in iTunes.)
4) AMF doesn't index attachments to Mail messages unless you download the attachment (presumably because it's then stored under your User folder.)
5) AMF will only seem to (sometimes) index Excel spreadsheets if they're saved as .xlsx files. Even opening, changing and saving a .xls file won't get it to show up in AMF afterward. Spreadsheets are strange, in fact. Even with some .xlsx files, they'll show up in AMF *while I have them open in Excel*, but as soon as I close them in Excel, they disappear from AMF again. This is the only types of file I've seen disappear from AMF after they've shown up once - all the other file types seem to stay in AMF once you can get them to show up there.