This was occurring in Mail.app 10.1 (3251) and is still occurring in Version 10.2 (3259) and is still occuring in Version 12.2 (3445.102.3)
When I view messages in the Archive mailbox, The entire message view (including the scroll bar) moves one pixel down and one pixel to the right and pops back. About 1x per second, possibly a little faster.
This interferes with interactions with the view, like clicking links or using the "load remote images" button. I usually have to click a few times as if the click target is disappearing at some point during the weird behavior.
Additionally when I am able to successfully click to load remote images the view usually reloads again without them, usually fast enough that the images never show up or are only up for a second.
If I move the message to the Inbox, I can interact with it normally. I also checked the spam and trash mailboxes and didn't see the behavior.
If I switch from Classic View to whatever the other one is called (Columns?) the 1x1 pixel movement doesn't seem to be happening anymore, but all of the other weird behavior happens.
I first noticed this behavior when I updated to macOS Sierra.
I do have multiple imap accounts and a gmail account that I think is also syncing using imap.
For now I work around this by moving messages I want to interact with to the inbox, but this is pretty irritating. Does anyone know how to get this to stop?
I finally got around to reporting this as a bug to Apple, Problem ID: 47550248