The form of your data in your original file, Error file.nb, is of the form

{
   {{_,_,_}...}
}

whereas the form of the data in your recent example file reply.nb is of this form:

 {{_,_,_}...}

When I take the first part of the data in your original file so that the form that is being supplied to the first argument of the NonlinearModelFit function is like the one in your second notebook, {{,,_}...}, then I no longer get the "non-negative numbers" message (but I do get a variety of InterpolatingFunction messages as well as some warning from NDSolve pertaining to some difficulty in the convergence of the numerical methods used by NDSolve).

I took a quick look at your notebook. However, it is hard to discern what's going on, partially because all the information needed is not there: i.e., Pdiff, Vb, and Fuc are not defined. Also you have two different numbers of arguments for Model3 in its definition (one in its left hand sice and one in its memoization internally). I cannot seem to get an example of just executing Model3 working... can you fill in the details and show some working examples of Model3 working?