Those 40c temps look a lot more realistic than what Sisandra was reporting. I've never really thought of sandra as a useful temp monitoring solution, but somehow the fact you were using that breezed past me before.
The best way to deal with case airflow, IME, is to have things set up to flow in one direction, ie front fans blowing in, rear fans and the PSU pulling air out.
A couple other things came to mind, one would be the capacity of your power supply. Those types of duallie rigs REALLY suck down the power. My dual MP 1900 system killed a 400 watt psu (fizzing, smoky death! hehe!) after about 8 months, replacing it with a high-quality 550 watt Antec solved that problem.
Also, some boards (like my now evicted Tyan Tiger) have issues with the number of banks of memory installed. That thing would never run stable with four DIMMs installed (1024mb), I had to settle for running three (768mb). It's possible one or more of your DIMMs has worked itself a bit loose, or is beginning to fail. Reseating your memory, and testing with
Memtest86 should help you check this.
Some (a lot, actually) of those dual AMD boards are quirky in their own strange ways, and one other resource I can point you to for more specific info would be
2cpu.com, particularly the forums there, for info on your board, and dual systems in particular.
Good luck with getting your system stable, nothing about computing is more personally demoralizing to me than trying to deal with flaky, unstable hardware you can't trust not to suddenly crash on you when you need it the most.
Oh, if you post what actual brand and model of system board you have, I or someoneelse might know of a particular issue with that board. (boy, do I know about weirdness with the Tiger. -_-; )