I have the MSI s939 Neo Plat 2 board with the corecentre that runs in background.

The problem I am having is that the corecentre alarm goes of and shows the 3.3 rail is running at 2.93 volts and fluctuates. What is causing this and is there a setting I can tweak to bump that up, I suspect it may be due to the cool and quiet program but am not sure...

Use a digital multimeter to measure your voltages. Software monitoring programs are dependant on the onboard sensor chip, which can vary widely in quality.

Where do you measure the 3.3v Rail with a MultiMeter?

I know where to measure the 12v & 5v, and there spot on, just wanna see what my 3.3v is

From what I remember you have to poke the 20 pin ATX connector at the orange wire...

http://xtronics.com/reference/atx_pinout.htm

Meh, I don't have a digital multimeter so I will just trade this PSU for a new 450 Watt I have in stock for an upcoming rig I will be building.

Is there a way in BIOS I can increase the voltage on my 3.3 rail?

You cannot adjust the 3.3v rail within the BIOS. The only way to adjust the 3.3v rail is if your PSU has a voltage pot inside (or outside the OCZ Powerstream). I would still get a digital multimeter even if you are getting a new PSU. It is a cheap lifetime investment.

I wish every(all of them) manufacturer add those trim potentiometers in all PSU they make, it's as cheap as gravel and does wonders