Cpu heating up-please help

HI,
i had a old Intel Smart Fan the porblem is,when i start my Pc it Stuck so i bought a new one and pulled out the old one,replaced it with the new one and applyed a Heat sink, then the problem apeared when i was in the Bois Screen in the Pc health thing my Cpu Temp is rising like a 1C every one Sec till it goes to 80 C+, the Wierd thing is that the fan Rpm is 2400+
and the Cpu Still heats up, i rapplyed a new heat sink and still the same,
the Wierdest thing is when i Start My Os/Windows it goes down to 50-60 C, if i stay in the Bois Screen it Goes up to 80 C+, so why is the Bois is heating up my Cpu? it was on the old fan after its failer about 45-50 C in Bois and Windows.

i have a ....
intel pentuim 4- Cpu 3 Ghz
160 Hd+80 Hard Desk
3Gigs of ram
Nvidiea GeForce 8400 Gs
sumsung Dvd writer
2 fans- 1 works as a normal fan and the ather works to Pull out the heat from inside

Note: the temp Gone higher when i Bought the new fan...

please help,thanxs