I am having the same issues with Mail, however, I am using the Mac Desktop. I have no rules to delete the messages, but since their last update many of my messages end up in the trash folder. Once I select all of them and force apply the rules, then they go to their proper folders, however, sometimes, they go back to the trash again unless I create a new rule memorizing the the e-mail. This is happening a lot with new e-mails whose address is not in my contacts list. Again, this just started happening after the last update. I am running Mac OX 10.9.4 and Mail Version 7.3 (1878.6). Any ideas how to fix this? I even tried to go to an outside programme but it is too much trouble since most of them do not import my mail folders and subfolders. Thanks for all your help.
Sorry, I was responding to the link and did not realize this section was for the iPad.