Apple Mail won't remember "Use this mailbox for ..." state

I have all my devices up-to-date now, with my two Macs having the newest versions of Lion installed.
I am trying to set up all my devices (2 Macs, iPhone, iPad) in a way that all my sent mails, drafts and deleted messages are always stored on the server.
To do this, I have to define folders like the "Sent" folder in each email account (on the server) as the one to be used as the Sent folder on the Mac - quite easy. (From the Mailbox menu, I go to "Use this mailbox for ..." and then define what it should be used for).
This worked fine on the MacBook Pro, and the iPhone/iPad (in the same iOS settings).
Somehow though, whenever I define this on my Mac Pro Lion installation, it will revert to the old state (save them only on the local disk) whenever I restart the program. It will go back to saving the sent emails and drafts on the local disk, and all the folders reappear in the dropdown menu under the individual accounts on the right-hand side in Mail.
It takes quite a long time to quite Mail too (although I am using an SSD), and Safari has been acting up lately as well (it goes back to a application state from January 4 whenever I restart it, so I see tabs and windows I browsed on that day). This might have to do with the fact that I copied my Keychain from my other Mac to the new one, but I can't figure out why ...
Any help would be greatly appreciated, it's driving me nuts because I need my email to be in sync at all times!

Who is your email provider? I only ask because depending on who it is, you may or may not be able to do anything about the next paragraph.
What method are you using to fetch your mail from the server - POP or IMAP? For what it sounds like you're asking to do, you should be using IMAP (which will keep things in check on all devices in all locations.) POP tends to be an all or nothing type of thing.
Any time you start transferring things from other Macs (like preferences), you're asking for things to start acting odd.

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Mail has to store those messages somewhere. Hence, the only way to “undo” those selections is to do Mailbox > Use This Mailbox For on a different mailbox or to turn OFF the corresponding Preferences > Accounts > Mailbox Behaviors > Store messages on the server setting.

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Alright, so, I have been playing with the updated Mail application in Lion. I love the new interface but I seem to be missing an important part or just unable to find it. When setting up an account to connect to Gmail's IMAP I seem to be unable to get the common folders, Sent/Draft/Trash/Spam, working in unison with Gmail's Sent/Draft/Trash/Spam labels. In the previous versions of Mail I've been able to right-click each of those folders and click "Use this mailbox for..." to which I would select the proper folder. This option seems to be missing in Apple Mail 5 or, the very least, I'm unable to find it or an equal option.
When creating an account to use with Gmail I have played with the preference checkboxes for those common folders. Leaving them checked I will get a new label created in Gmail instead of the email going into the real folder. For instance, if I delete an email it will go into my trash on the mac and it will then have the label "Deleted Messages" but not actually be in the trash in Gmail. The same goes for Sent Mail as well. If I uncheck these options then I get duplicate email in the Mail Sent folder as well as Gmail's Sent label. On top of this, if I click the sent button I in the new Mail interface I ONLY see mail I have sent from Apple Mail and not items that are in my sent mail label for Gmail. Which is annoying.
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If this has been asked and answered/resolved can I please get a link to the discussion? I've searched but seem to be unable to find any possible answers.

It is an exchange account. In Mail>Preferences>Accounts I do not see the IMAP Path Prefix, which isn't surprising (when it is no IMAP-account).
Coming to your question, Ernie: I created this account longer ago, maybe 2 years? I created this subfolder from a Windows computer and recently made the swith for my business computer to a MBA. Great computer! Strange thing is, the mails in the subfolder are shown correctly in my iPad Mail app... Also: I created such a subfolder in my Inbox and this mail is shown correctly... Strange... For this mailbox (and for all others) the options in the dropdown menu 'use this mailbox for' etc are all greyed out...

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Hello, all:
Have been using 10.6.x since it came out on my previous iMac [24" Early 2008 model]. Went with a fresh install of 10.6.3 on the new iMac [27" i7], and ported data over.
The only problem that I've had is that setting the Use this mailbox for Junk command in setting up Mail 4.2 does not seem to work. I've closed Mail and looked at ~/Library/Preferences/com.apple.mail.plist, and the correct mailbox name is indicated for the two accounts [IMAP and GMail over IMAP] where I'd like to do Junk Mail filtering. However, there is no centralized Junk Mail filter, which is really annoying me.
I didn't have this problem previously in Mail 4.x, and I'm expecting that it's a bug specific to 4.2, which I haven't seen in my previous incarnation because I did the import from 3.x->4.0, and the prefs carried forward correctly from 4.0->4.2.
Anyone else running into this, and is there anything else I should be looking at? Am I explaining the problem such that it's clear what I'm asking?
Thanks,
Geof

I figured out the problem (for me, anyways). In Preferences > Junk Mail, make sure Junk filtering is enabled and make sure the "move it to junk mailbox" radio button is selected.

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Hello!
I have a Mac Pro and MacBook Pro, both running Mountain Lion. My two Yahoo mail accounts are successfully set up via Mail on both Macs. I was able to use the "Use this Mailbox for..." command to assign the Drafts, Sent and Trash for each account to the respective Yahoo folders (so I don't have duplicate folders). The problem is trying to do the same for the Bulk Mail folders.
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I'm sorry it didn't work for you. I'm not sure but I think I deleted the account from the Internet Accounts preference pane instead of from Mail's preferences. Could that make a difference?
Anyway for me the behaviour isn't consistent at all. In three IMAP accounts one does't have the problem at all, one shows the "Use This Mailbox For" options "Sent" and "Junk" selectable and the other two greyed out, and for one account only "Junk" is selectable.
Strange.
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I am using the same version of OS X, the same version of mail and exactly the same setting in mail preferences. I don't understand why I can't get the Spam folder to be used as Junk? ANyone out there got any ideas?

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In mail under the mailbox menu, there's an item titled "Use This Mailbox For". All the options are grayed out. Why?

It still doesn't explain why the contents of the "use this mailbox for" is greyed out.
I noticed it first when installing Gmail (Seamless) but the same happens on Apple Mail.
In fact the number of greyed out submenus is quite impressive, and not just due to items not being highlighted.
it seems to me that some features were not activated during setup.
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Hello.
This question has been asked before, but has not been asnwered that I can tell.
My question is not "what is this menu item for?" or "How do I use this feature?" ... the issue that I am having is that the options are all unavailable when I try to use the feature.
Not looking for workarounds or other optoions ... I would really like to know why I'm seeing what I'm seeing, and what I need to do to get it to function.
Thanks!
-Travis

I too have this problem. I was trying to allocate a mailbox for Spam messages but all the options as you stated are greyed out. I have search all over the place and cold not find a answer for this so I was wondering if many others are affected by this.
So I took a look at my wifes iMac and her mail application and she has the same problem so it is not an isolated one that I can tell. I phone my son who has a Macbook Pro and he reported the same problem, what the heck is goining on here?
I and my wife use MAC O/S 10.8 Mountine Lion and my Son uses 10.6 Snow Leopard with the latest patches.
NOTE: I just found out why they are greyed out within this article http://goo.gl/HbR6f as we were using local mail boxes.

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This is the action that I'm talking about. I set certain Gmail folders to be used for these 4 options. I would like to release those folders from their respective duties.

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