I had exactly the same problem! I normally convert my HDV from the M10 deck through Convergent Design's HD-Connect to uncompressed HD for acquiring into Media 100 (11.5.1) because that is the best away to avoid GOP compression problems. However when I only need an SD timeline I tried to digitize a downscaled signal from the deck into Media 100. I got the same message as you. I finally abandoned this route and transferred the downscale to my DSR 20 deck and then digitized from that to Media 100, no problem.
Aha! So I'm not going mad! But what still remains a mystery is why the first hire two weeks ago went without a hitch, and this one worked, but only after fighting with it for hours.
I reckon there's a bug in the routine when Media 100 interogates the deck over the firewire to get its ID (for that drop down menu in the preferences). It might be a "luck of the draw" situation as to whether it correctly guesses the standard.
I'm guessing this is a PAL issue, as I doubt it causes a problem if the material is actually NTSC