This is a strange issue. Sometimes I cannot Clear the value of a constant and the subsequent calculations seem to lock the value in. Also, I have run into instances where dividing using " / " works then stops working and I have to put the complete denominator in as multiplication time the expression raised to the negative one power, and then it works again.
Is there some more powerful "clear" function that I need or is there some other "trick" I am missing? I have run into these issues in the past occasionally and it seems to "clear itself up" after a time.
To find this problem, you (or someone else) will need to make a compact example showing the problem. I assume you have already tried ClearAll and its relatives.
The most likely case is that you do not understand scoping well enough to find the problem in your code. Of course, Mathematica scoping is not an easy subject.
Make a small sample and then someone can show you some ways to expose the "Context" your code runs in.
Also try this: http://reference.wolfram.com/language/tutorial/Contexts.html