I snowboard a tremendous amount and have tought many people. Your experience is typical.... Even with a great teacher newbies spend their first two days eating it!
In addition, the critical frequency for the ionosphere is ~10MHz (that is, above that frequency, you can't really bounce a meaningful amount of energy off the ionosphere, most passes through). 10MHz = a wavelength of 30m. So in general, you'll only be able to detect things about 100ft or larger in size (and that's a lower limit-- practical is probably bigger). I'm not at all surprised that you'd need line of sight to track a plane. Knowing that there's something there is easier, but tracking is trickier.
I bet that during the initial design phase, they wanted to keep the design simple, have enough timekeeping range to cover the mission and then maximize temporal resolution.
Someone realized that a counter operating on tenths of a second from 2000 was both easy to use and sufficient for the primary mission... they then thought nothing of it until the loss of contact