Stopping Messaging pop-ups

Background IM check can be set from the config file using these following configuration

 
// Background IMs check mode.
//  0 - do not check for new IMs in background at all
//  1 - check for new IMs in background and if new one found, show popup window. If popup blocker blocks popup, show inline popup (floating DIV within a page)
//  2 - check for new IMs in background and if new one found, show inline popup (floating DIV within a page)
//  3 - check for new IMs in background and if new one found, only make "new message" icon blinking
$cfg_allow_background_IM_check = 2;

// I-Messages recheck period, in seconds
$IMSG_RECHECK_PERIOD = 30;

// $cfg_default_notification_method specifies default notification method for user
// This value is used only when a new user is being created
// Available values: "im" | "im+email" | "email"
$cfg_default_notification_method = "im";

// When to disclose sender's email in 'Reply-to' field when Instant Message is sent by email
//
// Possible values are:
//   IM_REPLY_ALWAYS - always shows reply to field
//   IM_REPLY_SAME_AREA - shows reply to only if message sent inside one area
//   IM_REPLY_PRIMARY_AREA - shows reply to only if sender or recepient or both are from primary extranet area
//   IM_REPLY_NEVER - never shows reply to field
$cfg_im_email_disclose = IM_REPLY_ALWAYS;