Well, add me to the list of people having this very same problem. It didn't happen until I created a CM10 partition and noticed the docks would not launch at all from CM10.
I went back to stock 4.1.2 via RSD Lite (stock stock, no root) and have the same issues. I have a lapdock and two vehicle docks, none of which launch into anything (charge-only). What's really weird is that in either of my vehicle docks, apps like Waze will not rotate to landscape mode.
I did try cleaning out the contacts on the phone and one of the docks, thinking it was a connection issue (after reading that the docks launched via some USB connection and no longer via magnets like the OG Droid). I used magic juice (electrical contact cleaner) and have had no luck.
Clearly, with two vehicle docks, I am very dependent upon using apps like Waze during my commute, and have been missing the vehicle dock functionality since I've noticed it was gone w/ CM10. (fwiw, it was 10.1.2)
(edit) Looks like on similar phones, the pds partition is the culprit?
Docks not working 