Never used an external with either of my S1 or S2 DT units. I've had that behavior from screwed up internal TiVo drives, and I even saw the "missing external drive" screen once on a Series 2 Dual Tuner, which I'm pretty sure isn't designed to be used with external drives.
I suggest you consider picking up a new internal drive while you're at it. It may actually have had whatever the problem was that the TiVo managed to fix.
(and consider skipping the external drive and using a computer with a big hard drive running Tivo Desktop instead)