Since you didn't claim you actually are missing mail, just seeing more
Nope. As I suffer the same problem from Evolution and ThunderBird
They could be "deleted" (actually marked for deletion, physically removed upon expunge). Those would have a T flag in the file name after the comma. Your MUA Evolution shows them in the Trash (virtual) folder.
I tried all this but nothing shown. It's like cur folder is not shown.
They could have been flagged Junk, and only be displayed in the Junk (virtual) folder.
Junk folder is almost empty since I have SpamAsassin in place
You could have a search active, hiding some mail.
I checked this also. But's not.
You could have specifically hidden them. See the View menu.
I checked show all. But only a few appears. The one deleted by spam filter in the client.
What else can be?