Advanced Settings do not stick!!!

Why do my "Advanced" settings change or come unchecked!! It is getting quite annoying. I check the box to remove ALL emails from server "right away". days later, all of a sudden all the same emails from the morning come down AGAIN. I go to my settings and sure enough, the box is unchecked. What up with this??? Also, getting annoyed with the need to check mail again before it will allow me to send a new message. HELP!!

For the first problem, it sounds like there might be some minor corruption to the Mail.app preference file.
Regarding the second problem, does your ISP or email account provider require POP before SMTP authentication which means you must login and check the account's incoming mail server for new mail before you can use the account's SMTP server to send mail but this should only be required once per login session (without quitting the Mail.app) and not each time you send a message. Has this always occurred or a recent change?
To target the Mail.app preference file, do the following:
All account information is stored in the Mail.app preference file located at Home > Library > Preferences > com.apple.mail.plist.
Unless you have a backup copy of the preference file that is working properly, this will require re-entering all email account information.
With the Mail.app quit and using the Finder, go to Home > Library > Mail. Copy the Mail folder and place the copy on the Desktop for backup purposes.
Using the Finder, go to Home > Library > Preferences > com.apple.mail.plist. Move the com.apple.mail.plist file to the Desktop.
Launch Mail and decline any prompt to import mailboxes. After re-entering all email account information the same as before, the Mail.app should rediscover the existing account named folder(s) and mailboxes at Home > Library > Mail.
If you have a .Mac account, the .Mac account information will be re-entered automatically. If you don't have a .Mac account, the email account you provided as part of the setup assistant will also be entered automatically. If so and you no longer use this account, you can delete the account from within Mail.
After confirming all mailboxes were successfully rediscover, you can delete the copy of the Mail folder and old com.apple.mail.plist file from the Desktop.
I've been using the Mail.app exclusively since Jaguar was introduced, thru Panther and now Tiger and although I've never experienced a problem with the Mail.app preference file, I include the preference file as part of my regular backup.
You only need to replace the backup copy after making any changes to account information or after deleting or adding a new account.
If this occurs again (which it shouldn't be a regular occurance), you'll have a good working backup copy of the com.apple.mail.plist file to replace the existing without having to re-enter all email account information again.

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