Apple Mail Behaving Strangely

I am having an ongoing issue with Apple's Mail program. Messages repeatedly show up in it as the wrong emails, ones that I had earlier deleted. The messages will appear normal on my phone and on the web version of iCloud mail, but on the computer they appear wrong, as if there were a corrupted cache file or some similar problem. If I move the message on my phone or on the web and then move it back, it will then appear normally. The problem is intermittent but frequent, and I can't necessarily recreate it intentionally in order to test it. I spoke with support for a while about this, and rebuilding the mailbox seemed to fix it as "broken" messages changed to display the correct content, but soon after that the problem reappeared. I have scanned for viruses, repaired permissions, cleaned caches, etc. to no avail. While not a terribly harmful issue, it is nonetheless quite irritating. Does anyone have any suggestions? (I am on OS 10.11.5 incidentally.)

Guy