Changing some of the keys passed

Okay,

Here is a rather odd problem that I cannot seem to work out. I use keyclone (Windows 7) and everything works great on my main.
The problem is when I mouse over to the other client it starts changing the keys passed. 'q' and 'e' change to ',' and '.'

So on client one if I press qweasd it will pass qweasd. If I am on the other client then try the same thing it passes ,.easd.

It is a rather annoying problem since I cannot use wasd to move on my main with this bug. On my other dual box characters I do not seem to have this problem, I have no idea what I could have done to cause this.

Thanks

Do you have any hotstrings set up?

Those specifically change a given key, from whatever on one window to a different key in another window.
That's about the only thing I can think of.