Please check your iTunes settings to ensure that "Disk Mode" is enabled for your iPod. This enables third party devices to interact with the iPod.
You will also want to ensure that iTunes is not configured to automatically update your iPod. If iTunes automatically syncs with the iPod, it will disconnect the iPod once this process is complete, stopping any other programs (including Media SOS) from using it. This is true even if the sync is canceled by the user.