slightly off axis

[wadeshuey]

I am working on a large store project and I have seen errors saying that your slightly off axis. Which I have checked and everything seams to be square. Now when I cut my sections I get all kinds of trouble. The align tool becomes useless along with I cant dimension. When I try dimensioning the crash protection pops up and asks me to save. And this is happing on every section cut. I am not sure how to fix it. And I am to far down the road to just redo the project. Has any one else had this problem? I Need help. I got a feeling that I'm in big trouble.

I am working in multiple phases It is old store that we are remodeling.

Thanks for the Help!

Wade