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
