Yosemite Mail preferences are not saved

Question

Hello,
I just update my Yosemite to 10.10.3.
After some problems with Mail, I've been forced to delete container files and enveloppe index file, all is better except that now mail doesn't saved preferences anymore..
Also, the windows positions are not saved as well...
Last information: ON my preferences folder, I got only com.apple.mail-shared.plist file, but no com.apple.mail.plist file... Doesn't now if it's normal or not..
Thanks for your help
Here is the transcript of my console file:
14/04/2015 18:00:18,388 com.apple.xpc.launchd[1]: (com.apple.imfoundation.IMRemoteURLConnectionAgent) The _DirtyJetsamMemoryLimit key is not available on this platform.
14/04/2015 18:00:20,841 WindowServer[157]: disable_update_timeout: UI updates were forcibly disabled by application "Mail" for over 1.00 seconds. Server has re-enabled them.
14/04/2015 18:00:20,856 WindowServer[157]: common_reenable_update: UI updates were finally reenabled by application "Mail" after 1.02 seconds (server forcibly re-enabled them after 1.00 seconds)
14/04/2015 18:00:21,066 com.apple.xpc.launchd[1]: (com.apple.imfoundation.IMRemoteURLConnectionAgent) The _DirtyJetsamMemoryLimit key is not available on this platform.
14/04/2015 18:00:45,888 WindowServer[157]: WSGetSurfaceInWindow : Invalid surface 1276785923 for window 508
14/04/2015 18:00:47,693 CoreServicesUIAgent[357]: unexpected message <OS_xpc_error: <error: 0x7fff76035c60> { count = 1, contents =
  "XPCErrorDescription" => <string: 0x7fff76035f70> { length = 18, contents = "Connection invalid" }
}>

Answer 1

But should I see a com.apple.mail.plist file ?
No, not in Yosemite.
Problems such as yours are sometimes caused by files that should belong to you but are locked or have wrong permissions. This procedure will check for such files. It makes no changes and therefore is not, in itself, a solution.
First, empty the Trash, if possible.
Triple-click anywhere in the line below on this page to select it, then copy the selected text to the Clipboard by pressing the key combination command-C:
find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \) 2>&- | wc -l | pbcopy
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad and start typing the name.
Paste into the Terminal window by pressing command-V. The command may take a noticeable amount of time to run.
Wait for a new line ending in a dollar sign ($) to appear.
The output of the command will be a number. It's automatically copied to the Clipboard. Please paste it into a reply.
The Terminal window doesn't show the output. Please don't copy anything from there.