Thank you for avoiding to clutter the post with loads of identical data. 
Just to satisfy my personal curiosity... (click for more)
What's trying to cloak g.msn.com?
Is it just a single domain?
You should be able to find out by expanding your grep for a few lines (e.g. 3) before the match:
grep -ni -B 3 "g.msn.com is blocked during" /var/log/pihole.log
The query [A] line should show the cloaking domain and the client that submits the query.
With your confirmation of a high number of entries, we can conclude that it's indeed handling of CNAME cloak blocking that introduced the glitch and needs improvement. That issue is currently dealt with by the development team (thanks to yubiuser for providing those links).
There's nothing you can do about it right now than wait for the next release, but it also doesn't compromise correct DNS resolution or blocking.