Thanks! If you want to try and find the issues in Blender you're welcome to it... I'm not too familiar with it myself and didn't feel like taking the time to figure it out when I posted this :P ; and I figured scaling the STL's in printer software will give reasonable results for most people.
If using slic3r I'd recommend combining a brim with a raft (only needs to be a few layers). This way the brim is on the raft, and the raft easily separates from the print itself .
This way you don't have to do the complex (and annoying work) work of cleaning the brim off the print.