I'm not quite sure what you mean by the data is inverted. Perhaps you could give us an example of the value you're seeing in Matrikon and the value you're expecting to see (i.e. the one in PI).
I think this might be better handled in a Tech Support case, but the first few things I would check are confirm the tag attributes such that it isn't configured to be scaled unnecessarily and also turn on logging for that point in ICU > UniInt > Debug to get a better idea of what values are being sent to the interface.
Thanks for your suggestion. I have found a solution, doing scaling in the Matrikon middleware. The problem wasn't really the historians it was to do with the data that came in from the field.