I guess I did not read your title clearly enough, and did not realize you were asking about HSM. I'm afraid I'm going to be of little help in that respect. The HSM (and SDM) use a different set of contacts to control the in lens focus motors (HSM is similar to SDM, Correct?). The 35mm Limited is a screw drive focus and is driven by the focus motor in the camera. One of the many complaints of SDM, is that when it quits working, there is no way to switch the lens to screw drive focus (if so equipped, the 17-70 and the 55 are not) and the lens becomes a manual focus lens at that point. It hasn't happened to me but has to others.
It's a REAL long shot but us there any chance there's an AF/MF switch on the HSM lenses that you've turned off? If you were using these lenses on a Pre-K10d or a K10d pre firmware 1.3, The SDM (HSM) is not enabled on those cameras so it may have been using screw drive. Just a couple extra thoughts..