Reverse scrolling strange behaviour

Hi,
I've thus far resisted upgrading to Lion (don't want anything to potentially mess up my thesis).
But I've been using Better Touch Tool in conjunction with a trackpad for a while (and have enabled inverse scrolling in the prefs). I actually like reverse/inverse/natural scrolling and find it quite intuitive. What I've been noticing though is that scrolling behaviour isn't consistent between apps. Scrolling is reverse in Safari, Preview and iTunes as examples that I've noted so far, but it's not reversed in Word 2011 or browsing the message pane in Postbox (strangely, browsing an actual message - scrolling is reversed again)
I have no idea what's going on - but it's a bit of a pain having to adjust to using 2 scrolling directions.
Anyone noticed anything similar.
A bug in BTT perhaps?
Thanks