If I scale an image in Premiere Pro CS3 (WinXP) then apply a RED 4.3.1 filter, the image opens in RED unscaled. If I then apply a paint stroke in RED, it shows up in the wrong position back in PP. Even if I scale in RED, the stroke never shows up in the right position back in PP.
The scale issue is a result of the fact that RED must take the media before any transformations take place. This is the render pipe that is passed to RED from Premiere Pro and you get around that by either performing all of the scaling in RED or by nesting / precomposing the scaled clip before applying RED (if indeed that is an option in the Premiere interface.
The paint issue is something that I'll have to look at when I'm in the office on Monday, unless anyone else reading this has any insight to offer. You might want to make sure that you are in full / high resolution in RED while creating the paint strokes.