MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Hey there, I'm currently using slic3r as well and have no problems to report. For these parts, I always include a brim because of those delicate first layers and out the top of my head this problem of yours might be due to resolution. If you haven't found a solution for it yet you can definitely print it with the rail facing downwards - granted there's a bit more of support material and cleanup to do and the pin holes will be a bit fragile, but it works all the same! I have some test parts printed in this configuration and my only complaint is layer orientation.
Let me know if I can be of further help!