Interesting temperature changes

So I've been having load temperatures of 56C on my Athlon 2000XP, this morning I decided to try something new.
So i opened it up, I put my Volcano 7+ fan on the stock Athlon heatsink. (my Volcano 7+ heatsink doesnt sit right on the CPU)
I sanded the heatsink with 1000grit, then 1500grit, cleaned it, then put everything back together.

Lo and behold, my CPU load temp is now 45C.. BUT! my mobo idle temp is 39C and idle temp for CPU is 40C

Isn't 39C a little high for the mobo? especially considering the CPU is only 3 degrees hotter.
What does this usually mean, bad airflow?
I've got one side intake fan, and one exhaust fan.

The Volcano7+ fan is on "highspeed" and is blowing ON the heatsink (not sucking air out, like the stock Volcano7 does)

Sounds like air flow problem. You are bringing air into the case faster and in greater volume than you can expell it. You can test this by removing a side paned. You will notice that CPU temps drop but case temps rise.

I see. What exactly is the danger zone for the motherboard? Not too long ago it was at 41C

Put a big 120mm in the front of your case and if ya can a 120mm or 80mm blowhole up top. That should give you enough airflow. My temps went fromn ~40 case temps to 19-24 just by putting a 120mm intake up front