When you are sitting in BIOS Setup (Visual BIOS), all power management features in the processor are disabled. As a result, the single core that is running is doing so at its highest supported clock speed. Further, all interrupts are disabled; the firmware is running single-threaded and, when there is nothing to do, the firmware sits in a loop waiting for user input.
When you are sitting in Windows, typically all power management features of the processor are enabled and, while multiple cores are running (and possibly hyperthreading as well), these cores are able to lower their clock speeds to very low levels (even off). Further, interrupts are enabled and, while many tasks can be present, Windows can halt the execution of tasks that currently have nothing to do.
Bottom line, you cannot assume or conclude anything when comparing the temperatures you see in BIOS Setup versus what you see at Windows idle.
Hope this helps,