Good idea, but that doesn't seem to be it.
* I've tested one end of the cable to the other, and traced the signals from the floppy disk to the right pins on the chips on the interface board.
* The monitor program launches, and I can stop/start motors, select the right drive (I've two connected), even step the heads in and out.
* The monitor program always reports "Please insert disk" when it does something such as reporting information that needs to know the speed. Putting a disk is not detected.
* My scope cannot detect a pulse at ATMega pin 19, nor on Pin 8 of the ribbon cable from the floppy.
* The drive select signals go high/low as expected.
* I built a second drive interface card as I was determined to rule out that I'd broken the first one. The results with it are identical.
* When I pretend everything is great and set up the AltairDuino to boot from floppy, the disk motor starts but there is no head activity (I don't have a known good boot floppy anyway, as the monitor program won't work to create one).
I've spent enough of my weekend on this for now, so I'll pack it away and maybe something will occur to me.
thanks for the suggestions though!