Thanks for the kind words about RailClone, We're glad you're enjoying using it.
Depending on the specific situation for your building, this problem is easiest to solve if the splines share a common corner. The problem occurs because the lengths of the splines are different and by default RailClone will try to even out the distribution of evenly segments along the spline to make the spacing at the beginning and end equal. This mode is called Justify and it is on by default.
If you switch it off, RailClone will space Evenly segments the exact specified evenly distance along the spline, starting from the previous corner. This image illustrates the difference between having evenly on and off:
Because the corner vertex acts as a reset, a common vertex is necessary, but it may be possible to add vertices to the spline to force the evenly segments to reset and all start measuring again from the same point.
If you'd like me to look in more detail at your specific case it is often helpful to be able to see the RailClone objects, please feel free to upload a stripped scene (just the RC objects and splines would be fine) or send them to firstname.lastname@example.org if you prefer not to share them on the forum.
I hope that helps.