Smart folder doesn't include all the files it should

I'm trying to set up a smart folder to show all .graffle (OmniGraffle) documents on my Mac modified within the last 7 days, but no matter what I do, there are many that don't show up.
Even if I just set up a simple query to show all .graffle files, it only shows me a few. There are whole directories it seems to overlook, but these directories aren't special in any way that I can think of. They just exist alongside the directories that ARE being indexed.
If I move the files into the other directory, they show up.
Any ideas?

The simple query I'm working with is just to search "This Mac" for the string "graffle" appearing in the File Name
It just seems to be certain OmniGraffle files that don't show up, Lots of older graffle files do show up; these are all in a particular directory. The ones that I've attached to email messages show up (as being in my "mail" directory). It's just the ones I've created in the last 6 months or so - all for one particular project and located in the same directory - that don't show up.
Just now I did a test where I created 2 new files and saved them to different places. One in the problem directory and one in a different directory, and I couldn't duplicate the issue. I made a new smart folder, and both files showed up. This leads me to believe it's an issue with specific files, not a directory.
So I did a test where I opened one of the problem docs. I made one minor edit and closed the doc. Then I made a new smart folder, and it showed up.
Finally, I did a test where I opened up one of the problem docs and immediately closed it. Then I made a new smart folder, and it still did not show up.
Next, I'm going to compare the properties (get info) of a problem doc with one that shows up in the query.

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