Or, speed limit?

I have a program that does a bit of computational fluid dynamics. A lot of math calculations, again and again and again. I estimate it does about a trillion calculations, and it takes 10 minutes. Ok, cool. But lately I have tried to add a few things both fairly minor (I estimate a few percent increase in the number of calculations). The calculations I have added were unrelated, and I double checked them multiple ways, and they are functioning as expected. When run on their own, they function normally at high speed. however when added to my main math section, not inside other loops or anything like that but simply added at the end, my program is now taking 2 hours to run. It seems as though I have reached a critical mass of program size and that adding anything else results in a massive increase in runtime. Anyone else experience anything like this?

Thanks