Deleting in Mail doesn't delete, trying to understand Smart mailboxes

So I'm trying to get my Mail down to Inbox 0. I have it in other applications that only link to my Gmail accounts, but I also have a couple iCloud accounts that don't link to this service and my Mail isn't exactly syncing with those now-zeroed Gmail accounts.

I made a Smart mailbox and discovered those emails in the Smart didn't disappear from general - when they went to the Smart, and when I deleted them from Smart. So I looked into it (here - yay!) and found out it's just a ghosting kind of thing, that I would need to setup Rules. Did that, creating actual Mailboxes for those to live because they won't redirect to a Smart (which is pretty stupid). They're still in their original locations, but they didn't appear in the new mailbox. I even selected them and clicked Apply Rules. Still there.

So I went back to their original locations and just tried a simple search, select, and delete. They're still there! I did it again. Still there. I selected Erase Deleted Emails. Still there! I even tried Apply Rules again. Still there!!

How in the heck do I get emails to show up only in one place, not in the Inbox, and to actually delete when I tell them to delete?

OSX Yosemite, 2012 Mac Mini w/Fusion drive (my processing power is not the problem)

First of all, the messages should be moved to the Trash if deleted from a Smart Mailbox. It works fine here on Yosemite- now. I'll explain below.

Sounds like some corruption is messing things up. When I first installed Yosemite the Smart Mailboxes didn't work at all. New rules didn't work either. Went and "repaired disk permissions" from Disk Utility as that has often fixed strange problems. Didn't help here. I tried everything I could think of, even rebooting the computer, no go. Two days later they started working and have worked fine ever since. Strange?? Sure is, maybe someone on this thread will have an answer. I sure don't. I was about to reinstall the OS over the top of the existing system, but didn't need to as it started working. I know it solves some problems for some people. Maybe it would for you.

How Yosemite handles mail has been a challenge. I had a lot of problems with gmail and live mail. Then a few days after I installed Yosemite 10.10 with the mail accounts set up but not working, everything started working. Mail arrived and I could send mail too. I have no idea why or how. Initially, I had tried all kinds of setup changes, deleting and re-setting up, etc. Nothing worked. Then it just did.

Do a search on this forum and you will find this has been a problem. Yosemite 10.10.1 has supposedly fixed any leftover issues with mail. If you haven't installed it yet this may help. I am just glad it did not mess up want miraculously started working.

Lisa

A Smart Mailbox is not actually a mailbox at all. It's the results of a search of specified "real" mailboxes of a certain criteria (for example "all unread mail that is older than five days"). So you can't actually delete something from a Smart Mailbox that meets that criteria until it doesn't anymore (in this case, once I read it the email is no longer unread and thus "disappears" from the smart mailbox -- having never left its original "real" mailbox at all!).

Hope that helps.

Thanks - glad to know it's not just me. Any recommendations for a better free client?

I would install the 10.10.1 update that Lisa mentioned and see how things go. There's a lot that I like in Mail, though it's not perfect. Normally it works just fine so I wouldn't jump too quickly. If it continues to give you grief then Thunderbird probably is the next best option. I've used it in the past and many really like it. I prefer Mail over Thunderbird myself, but that's just my preference.

Cliff