The Startup pane of the preferences window (accessed from the Preferences... item in the Music Rescue menu) contains settings for Music Rescue's behaviour when the application is launched.

If only one iPod is connected
If only one iPod is connected to your computer when you launch Music Rescue to bypass the startup window and go straight to the Main Window or QuickRecover. If so, choose the relavent option from this pop-up menu. If "Ask" is chosen, Music Rescue will still present the startup window and allow you to choose what to do with the iPod.
Queue tracks by default
If this option is switched on, Music Rescue will queue all of the tracks by default. Note: This happens before any RuleSets marked "Apply on Launch" are applied.
Check for Music Rescue updates
If this option is switched on, Music Rescue will check for updated versions automatically. Regardless of this setting, you can always manually check for updates by choosing "Check for Updates..." from the Music Rescue menu.
Warn if iPod type is unknown
If this option is switched on, Music Resuce will ask you the type of your iPod if it can't determine the type itself. You can optionally submit this information to us so we can improve Music Rescue's type detection in future releases.
Scan iTunes Library
If this option is switched on, Music Rescue will attempt to scan your iTunes library about the tracks it contains. Using this information, Music Rescue will then tell you if a track on your iPod is also in your iTunes Library or not. For more information on this feature, see the iTunes Integration section.
If Music Rescue cannot automatically find your iTunes Library or you wish to use a library other than the one active for your user, click the "Manual" radio button and choose the iTunes Library.xml file in the library that you'd like to use.