I simply read the First line of the post and gave my assumption that it was start up applications. Like I said joowan, the main cause of PCs taking too long to boot up is how the processor reads the memory and hard drive.
While part of this is true, it is not the only factor. Factors such as having external device plugged into USB Ports, WebCams and just about anything else that you have hooked up to the system matter.
The Drivers for these start to load up during the boot process. Which is why if you have any lights on things like a keyboard or mouse, you will see them flash. They are getting initialized.
My thought would be a outdated driver. Be it for the chipset or another device. Startup Applications dont take effect until after the login process starts. But there is still plenty that happens before it.