The new serial numbers started appearing in 2006 after Nikon announced they would direct their efforts to digital imaging, which was only DX format at that time. Most manual focus AIS lenses were discontinued, all film cameras discontinued (except F6 and FM10), and many AF lenses designed for film format such as 28-105 were discontinued. It seems that as part of the reorganization, serial numbers for most (all?) lenses were reset at that time.
Quite a few lenses also had new serial numbers in 2005 also - this series is obviously quite short lived, so these lenses are not common.
As far as I know there is no difference to the lenses over this time, only the serial numbers are different.