It's hard to tell what might be the cause from the picture but there are a few possibilities;
- If you are using half shingles in the left or right inputs to create the offset, check that their transforms match those of the full size tiles. It could be that their just rotated and offset differently
- Could it be that the geometry was scaled at some point? If so resetting the XForm of the segment sources might fix this.
- Check the pivot alignment in the segment's settings for the 1/2 tile.
If you could send me just that RailClone object then I'll take a look and find out exactly what the issue is.
I hope that helps, please let me know if you have any further questions.