Well even though Martin essentially answered this with a very educated guess, I'm entering this as an answer because it's too long to enter as a comment.
Here is the evidence…
• Indeed, 10.7 is when Auto Save and Versions was introduced, so that's why you don't see UF_TRACKED in stat.h in 10.6.
• I tried my experiment on a Mac running Mac OS X 10.7 and it behaves the same as in 10.8.
• There is a pattern: Document files created by some applications, which after examining a few appear to be those which have adopted Auto Save and Versions, are the ones which have the UF_TRACKED = 0x40.
• Another experiment. I renamed the revision daemon executable in Mac OS X,
/System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/Support/revisiond
then restarted the Mac, and monitored the UF_TRACKED state of a document file in Dropbox which had 0x40. I then changed the file on another Mac, so that Dropbox would push it to this Mac with the revision daemon disabled. Result: The UF_TRACKED state of the file changed from 0x40 to 0x00, but this time it did not change back to 0x40 after 2 seconds.
• It did change to 0x40 30 seconds later, after I restored the revision daemon to its original name, and it relaunched. (Apparently revisiond is started by launchd with a KeepAlive attribute.)
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So the evidence is overwhelming that Martin's guess is correct. It is Apple's revision daemon and not Dropbox which is setting UF_TRACKED to 0x40. The meaning of this bit is that its document revision is being tracked by Lion Auto Save and Versions.