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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!