When I disable the sync of the trash folder this problem does not occur.
The clue might be in that phrase.
So, what actually happens, if you "disable the sync of the trash folder"?
What happens to the messages that you delete in that case?
And two questions:
1. When you say "delete it" in your original description of the situation,- how do you have "delete" defined: (1) "move to Deleted folder first" (2) "Delete from the server immediately" (3) "Hide in the app, keep on the server"?
(You find this setting by long press on the account in the account list view -> Options and Folders -> Account options -> Deleting messages)
[And you can also choose any of these actions when you are deleting, - the two that are not set as "default" are in the menu of actions]
I suspect it is (2), but it would be nice to know for sure.
2. What folder do you have designated as "Trash"?
Are you sure that's the one that is designated for the deleted messages by the server?