If my experiences are anything to go by, your board is doing what it is supposed to. I have a similar setup to yours (MA790FXT-ud5P with Phenom II 955BE) and on initial install I get similar results (40-42°C @ 1.344v), but the processor in my case is running at full speed (3200MHz). The figures only came down when I installed and enabled the Easy Energy Saver utility. Once enabled the core voltage dropped, the speed dropped, and the temperature dropped with it. When I set it voltage level 3 and enabled CPU throttling I got to 800MHz, 0.896v and the temperature dropped to below 35°C. The CPU power consumption also fell from about 49W to about 10W. I am using the latest version from the website rather than the slightly out of date version supplied with my board.
What I suspect you need to do is three things. First, make sure AMD K8 Cool&Quiet is enabled in the BIOS (should be under Advanced if its laid out the same as mine), second load the Cool&Quiet driver from the motherboard CD, and third download and install Easy Energy Saver. Once you have done that, turn Easy Energy Saver on, select the desired voltage level (1 is the highest voltage, 3 the lowest), turn on CPU throttling and then close Easy Energy Saver. At this point it should ask if you want it to run in Stealth Mode. If you reply yes the utility closes, but the hardware based energy saving routines based on the last settings remain active, even after a restart. However, please note that the only way I have found to get of energy saving mode after a restart with it enabled and force the processor back to full speed & voltage is to go into the BIOS and disable Cool&Quiet. After starting up with it disabled, it can be re-enabled in the BIOS on the next reboot and the processor will remain at full speed. Obviously this is only a potential issue if you're doing anything that needs the processor held at full output, i.e. if you're planning to overclock.
Even with the temperatures you're getting at the moment, your processor is perfectly safe. The PhenomII range is rated up to 62°C. Also, my previous computer (AthlonXP 2000+ based) usually had the processor running around 55-60°C and it qwas still going strong after 7.5 years of use when I pulled it out of the PC a month ago, and I'm planning to use it as the basis of a simple server and retro PC for running older applications and games that need proper Windows 98 and won't work in a virtual PC. By that score, without any special treatment, the PhenomII should easily outlast the software that can run on it providing it is not heavily overclocked.
