i've noticed in these last few releases that the automatic checklist starts to pause for the next AGC light but then decides to carry on before it comes up causing an error when the checklist then presses pro. Here's an example of it from A7 29:29 where it was waiting a chunk of time for the mnvr to complete (F 50 18) and even though the AGC is still in 06 18, the checklist carries on. What's the issue here I know the computer is busy running a few progs but the checklist should just wait for the 50 18 and it doesnt.
To answer your checklist/CMC question, the auto checklist has a built in delay for some of those, its a fixed time and doesnt "wait" for the CMC but rather counts a certain about of seconds before proceeding automatically Of course, they don't always have the right time since the CMC might be busier. Nothing has changed with respect to this timing with the releases as far as I am aware.
In Apollo 8 and later checklists I made this a complete pause instead of a time delay, when we go back and look at Apollo 7 checklists, I will add this pause (yellow text) to F50 18's and other places where you might have to wait for the CMC.
For now, just turn auto off and proceed manually when the CMC is done.