From the “you can’t please all of the people all of the time” category 
I see the shadow is fixed for the top panel. But I liked the “flat” look of no shadow for my panel. Any chance of a no-shadow option?
which windows manager are you using?
Marco with its own compositing enabled.
It might be down to the theme you are using?. 
I was using the default before and after, but I did also try Numix. As far as I understand it, not having a shadow was a bug, and I think having it now is because it was fixed recently.
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Yeah, that's right I think. I remember reading about somewhere that some kind of delay was built into the compositing side of Marco in order for it to not get missed by the system at bootup. I am afraid i don;t have an answer vis a vis Marco with compositing enabled. But, I think that Marco with Compton does not have the shadows on the panel. Have you tried that combination in Mate Tweak?
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I forgot about that new option. I’ll give it a try.
That does remove the top panel shadow consistently for me. Thanks!
But, I don’t like the alt-tab as much 
Choices, choices…
(And I just realized, in case other people aren’t seeing this change, I do have the ubuntu-mate-dev/xenial-mate PPA enabled, which may have a newer ubuntu-mate-settings package that added the shadow back.)
You can also use Compiz without panel shadows. You’ll probably need to install compiz config settings manager. If you decide to go down that route, come back on here and I will show you which part to configure to ensure flat panels. I only know about his, cos I spent some fair time figuring out how to get panel shadows in compiz…
So, showing you how to disable them in compiz is just a case of reverse engineering
Thanks for the offer, but I’m on a Compiz-free diet
But thanks again for suggesting Compton. I had forgotten all about that being included now in MATE Tweak.
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Same here as it turns out. I am now on marco plus compton.