No - operational upgrades do not count for CoS bonus.
This weekend my partner and I did YYZ --> LHR and back and got operational upgrades both ways

and in both cases we got ML*1 added to the new boarding pass. No CoS added as expected.
AC's inconsistencies abound. On the YYZ --> LHR segment they called out our names in the T1 MLL for the upgrades. On the LHR --> YYZ segment this did not happen the upgrades were apparently called out at the gate and not the MLL -- we only found out we had J seats on boarding which was cool since we had row 30 on a 767.
Interestingly enough, in neither case did I bother agents about the possibility of an operational upgrade. We had $599 tickets so using upg coupons was not an option as I've tried before on cheap tickets and found AC to be quite strict on this route (I'm AC*E). However, I did know Y was full and J/C relatively open. To me this confirms the view that badgering the agents for operational upgrades really does not increase your chances -- the better strategy is to look for flights where Y is likely to be oversold and there is space in J.
[This message has been edited by ACORD (edited 04-18-2001).]