I am wanting to measure the performance of an algorithm which I've created, and for some reason the value decreases significantly as I run through my loop

With absolutly zero info about the algorithm, and absolutly zero code to look at, I doubt that anyone can explain your results. Can you explain your algorithm, and post all the relevant code?

I agree with JamesCherrill. You can't measure the performance of an algorithm without first understanding the algorithm.

It's like asking someone 'How long is a piece of string?'

Without the string, we cannot tell.