pROC and ROCR give different values for AUC

I considered that but on the list more people are likely to see it. So if they ran into the same thing they may already have figured out what is going on and have answers. 
Or if not, I'll make a reproducible example, ask the maintainers and post back here where others may find it.

(but not till the end of the week)

Why are you sending this to the Rhelp mailing list? You should instead be
reporting it to the package maintainers.