is this problem persisting in B1009.31.2 ?
Yes. I'm using Chains of War, Build 1009.31.2.
It's hard to replicate the guidance issue in a standalone test scenario (I tried to build one). But after I said I couldn't recreate it in earlier post, I ran into the issue multiple times in Chains of War. Bottom line is I think the loft logic is better than previous patches (I recall a recent update) but still not perfect. The missiles always tend to want to fly high, and the sensor cone has a hard time picking out a lower target. I think this is because it stops getting data from the guiding aircraft once the radar activates, which isn't true. Alternatively, if the target dives evasive, the missile should dive accordingly earlier, and the antenna seeker should be pointing downwards. Right now it seems like it's too easy to escape the cone of the seeker low, which is possible yes but not as easy as the game dictates, especially over open water.
As for the CEC issue, the scenario above should demo it.