Welcome to the differences between men and women. There was a reason the book Men are from Mars, and Women are from Venus sold so many copies. My only suggestion is to try couples counseling. Counselors kind of work like an interpreter.
Try this - Ask her if she trusts you. If you get a yes, without doubt assure her she's taking your words the wrong way. She what she says then. If she can't stop the misconstruing, then she may have a hang up about just wanting to believe what she wants to believe. I don't know for sure, but it could be a form of being a control freak. I'm not saying that she is, but what do you think? Again, not to imply, but there are many people in the world that think the rest of the world is wrong if others dont think the way they do.
All the best. Hope divorce court says out of the picture.
There is another simpler book which you can you for a quick fix about your problems with communication.
"WHy MEn don't have a clue and why Women always need more shoes", by Marbara and Allan Pease.
GO GRAB GET THIS BOOK!
Here's what can help you for the time being
We guys normally mean what we say....i.e we use direct words
But women often use indirect speech, specially betw themselves, and they forget that man are not women, so when you are saying something, she tends to hear sthg else.
Tell her about that too.
WOmen deal with stress by talking about it, withouht requiring you to input solutions, where as Man prefer to be alone and think about it. Let her know that as well, as if you are not talking to her, she might immediately assume taht you are angry at her.
IN anycase, you wil HAVE to get "Men are from Mars Women Venus " in the end. Go read it, AND BOTH OF YOU