Heat = Laptop ?

The upcoming final release has a throttle function. Already the website device profile allows to enter the required value (1st option i think). Version 5.8.4 is just out, but still not declared gold.

There are several utils that achieve what u want:

Threadmaster: For the studious type and not shy and fearful of Register editing. Very smooth throttling on multiple apps even one could run HDC at 60% and GC and 90% e.g on a dual core.
BES: Has a graphical interface, Fabrique en France. Not tried it, but it allows the direct process selection from a list of active processes. http://mion.faireal.net/BES/

The BOINC throttle will work on the basis of the percent off and on as at 60% it will work 0.6 seconds then pause 0.4 seconds (could be 6 seconds on 4 seconds off as well, but not tried).

cheers

Did u select the BOINCmgr.exe or BOINC.exe? The one to choose is WCG_xxxxxxxxxxxxx_intelx86. Assuming you did take the latter, that's a pity to hear it's not doing what's expected.