positive class in logistic operator? Disagrees with AUC

First off, I want to thank everyone here, ESPECIALLY SIMON, for all the great help with my last question.  I couldn't have gotten this far without you guys!!

My next question should be much simpler...

I am following a suggestion read in a paper to use a "conditional logit" function for some training.  This leads to two questions:

1) Is there a "conditional logit" function in RM, or is this the same as the W-Logistic operator??

2) I learned in the past how to indicate which class is positive and which is negative in RM.  There seems to be a discrepency with how RM handles it.  In my current process, I indicate the "not sick" class as negative by making sure it is the first label in the arff file.  The problem is that the performance classifier and the w-logistic operator seem to disagree on this:
      a) The AUC for the binomial performance operator correctly states "sick" as the positive class and draws a nice curve for it.
      b) The resulting model for the W-logistic operator indicates the "not-sick" class as the trained for class.

This seems wrong to me.  Shouldn't the two operators agree on what is the positive class??

Thanks!