If you have MailScanner running in the background, one issue you can run into is duplicate emails.  Try the below to see if it fixes your issue:
PROBLEM
Receiving duplicate or repeating e-mails in your inbox.
SOLUTION

Linux OS does a superb job of handling sound.  Since early on it will even be configured out of the box.  Unfortunately, keeping it that way is an entirely separate matter.  Especially when going through multiple upgrades or installing other packages possibly even applications that may alter your sound behaviour strange things may start [...]