I recently replaced the Athlon 64 3200+ CPU in my Asus A8V Deluxe with a dual-core 4600+ (I was lucky to find one of these nearly-extinct Socket 939 creatures). I have the latest BIOS (1017), which I allowed to configure its automatic settings (no overclocking or plans to do so). When I got everything set up, I ran CPU-Z. It told me that my RAM was running at 166MHz. It also confirmed that my 2G of Kingston ValueRam PC3200 (4 pieces of KVR400X64C3A/512) was rated for 200MHz (DDR400). So I went into BIOS setup, changed "Memclock Mode" from "Auto" to "Limit," and set the speed to "2:1 (DDR400)".
CPU-Z now shows a memory frequency of 200MHz, and Windows seems happy with it. The other memory parameters that CPU-Z shows haven't changed. I believe that I've merely reset the RAM speed to its correct full rating. But could there be a good reason for the BIOS apparently underclocking the RAM in its automatic configuration?
Most likely, your bios reverted to a safe speed with the new hardware to guarantee that you could boot. If you are concerned that your bios is not detecting the hardware correctly you could clear the CMOS and see what it resets to.
Some MBs are only rated for a max speed of DDR-333 when 4 DIMMs are installed, but will run at DDR-400 when 2 DIMMs are installed. Your system sounds like its working OK, but run memtest86+ and something like Orthos, dual PRIME95, or other CPU/RAM stressor to make sure.
Yes... that would be the A64 4 DIMM memory bug. When 4 DIMMs are installed on older BIOS's, the memory downclocks to DDR333. It can be forced to DDR400 though. Most motherboards sold now have the fixed BIOS.
Regardless you're good. Just remember to force it back to DDR400 when/if you clear the BIOS.