Does riding a cyclo cross bike carry a large aerodynamic penalty when compared to a road bike? During club rides I find myself getting dropped by riders with the same weight and power but the main difference is that they are riding road bikes and I am on a cyclo cross bike (with road tyres and wheels). 

Is it my position on the cross bike or is it almost impossible to make a sensible decision with out knowing my co efficient of drag area? 

The current bike I have is a merida cyclocross 3 with cantilever brakes (pictured).
On a cyclocross your CD (drag coefficient is not much different).
You are the same basic shape.  

It is a little taller so you have a bit more more frontal area  

Are you sure you are the same weight and power? Would any of them be willing to swap bikes and test.

I get dropped on rides on my street CX but it is because I am just not as strong.  

Based on your comment I think you are confusing CD with area
Drag = CD x Area x Velocity x Velocity   

If you are getting dropped while drafting as a team (they are not trying to drop you) you cannot blame that on aerodynamics. 
The guy(s) in the front have more more drag than you even if you are sitting a little taller. 
If you are getting dropped you are not helping the team.  Take a shorter turn when you are in front.  Try and line up behind the next tallest rider.