You probably need to change the metadata plugboard, but the reason the next book replaces the book already on the device is the save template. This is set in the driver configuration. For this I have:
Code:
{author_sort}/{title} - {authors}
With that, if I was sending a book to the device with the same author and title, the second would replace the first.
To distinguish them, you need something extra such as the series info. The following should work:
Code:
{author_sort}/{series}{series_index:0>2s| - | - }{title} - {authors}
If this has stopped working recently, have you changed driver? If you changed from the KoboTouch to the KoboTouchExtended driver or the other way, you will need change the save template in whichever driver you are currently using.