Boot Camp startup problems when using "Startup Disk" but not when using "Option" key on startup

There are essentially two ways to start up Boot Camp (mine has Windows 7 in it). The first is to open up System Preferences, click on "Startup Disk", then choose the Windows partition and click "Restart...". The second is to restart the computer then hold the "Option" key, then select the partition you want to start up in.

For some reason, if I use the "Startup Disk" method, about half the time I will have problems in my Windows 7 partition, such as all icons in the system tray being invisible, my two displays changing from "extended desktop" to "duplicate desktop", etc.

I have no such problems when I start my computer up using the "Option" key method.

Could someone tell me what the primary differences between the two methods are, which could help lead me to what the potential problem might be?