I would suspect that there is a hardware something going on, point of sale machines are not designed to a typical PC spec
The newer version of NAV uses a newer dot net framework which required more resources to load,
An example will be that windows 3.1 will load a lot faster than windows 7 as the software is smaller, however you cannot do as much with win 3.1
Short of a hardware upgrade i don't think you will be able to speed up the boot time