This morning CHKDSK ran on its own during boot. It scanned 1 out of 3 HDDs in my PC. Is it a warning sign that that particular HDD is about die?
Chkdsk is automatically run on a few conditions, the most common being an improper startup/shutdown sequence.
In case you did this and forgot - Chkdsk can also be run on startup if you tried to run it when Windows was running, but Windows could not lock the disk. In this case, it will ask you if you want to run Chkdsk at startup, and if you click 'yes', then it will run before Windows starts.
Most likely it's the first case - an improper shutdown/startup. But to answer your question, no, Windows/chkdsk does not know about the condition of your HDD before it runs. It is running because it made some assumptions that a sequence of previous events may have left the data on your drive in an inconsistent state.
A patition's dirty bit could get set because of both hardware ans software problems, although I wouldn't call it a problem if it was an isolated incident and Chkdsk didn't find any errors.
Keep in mind that Chkdsk only checks the file system, not the HDD itself.
To verify that your HDD Download a S.M.A.R.T. tool (e.g., Passmark disk checkup). These tools report on several indicators of imminent failure, such as a high reallocated sector count (sectors that have been moved to the spare area due to read/write/verification errors).