How close are you to the ships in question, and what is the weather like?
One of the frustrating things about auto-TDC (I use it as well) is that it doesn't 'see' a ship until it thinks that a random crewmember on your ship can 'see' it (like, whomever is manning the periscope while you're at the nav table). Using the bridge TDC, with it's high-zoom factor, you can usually see about 4-5000 yards on a clear night, but it won't appear on the TDC until it's on the low end of that scale. In stormy weather it can be much worse...i've had ships close to within 700 yards before the TDC picked them up.
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