Originally Posted By: Archeon
After 10 minutes, all of a sudden, the files popped up! Now, all files can be found, just like it should be. Yay!

So my guess is the mac was still indexing the files or something. (shame there is no indication of it being busy with this task anywhere!)

Spotlight used to have an indicator when it was still working on a large indexing operation such as the first scan, I'm not sure why it's faded away with more recent OS releases.

If you want a hint that indexing is running, you can open up Activity Monitor and search for processes called "mdworker" using the CPU. You should see at least one, and if under the View menu you turn on All Processes, one or more per user on the machine tends to appear.