Well eventually I came up with the solution.
So, one of the times I went to windows 7 to install updates and configure everything, i must have gone to the windows control panel and clicked on the Boot Camp icon to see what it was. And I must have messed with it and clicked on the Windows Partitition. When you click nothing happens but it stays clicked and that means windows (Boot Camp) will be the default boot partitition leaving rEFIt on the shadow :P
Not very clear information about this, and specially the control panel application if definitly not clear about when it's clicked or not.
Anyway, I hope it helps somebody. I spent a few unnecesseary hours after the solution.