Oops. I just realized that the “file number reset” setting on my D90 was set to off, because I got a new camera and assumed the default was correct, because it is on the D700. It’s not.
(Background: The “file number reset” setting, when on, starts over with the same default filename, DSC_0001, every time you use a new or erased memory card. If you turn that setting off, the number counts up indefinitely, even across memory cards, unless you explicitly reset it. I much prefer the no- reset mode, so that each picture I take gets a unique filename, or at least a filename much more likely to be unique. The D700 I use most often ships with “off” as the default, which is good; the D90 still ships with “on” as the default.)
To fix this on the D90, go to the custom setting menu, area d, and find setting d7; turn it off.