The RailClone clipping is based on Max booleans, that unfortunately not always work as intended. I'm afraid there is not much we can do about it.
In this case, if you need clipping only to create shorter start/end pieces at the first rows of the array (as far as i can see from your clipping spline), it can be done using a Sequence on Y. Just set the first counter to the number of rows you want to change, and the second counter (for the rest of array) to a high value (as 99).
The shorter left side segment uses a Left padding to get the effect. It's necessary to create a similar piece for the right side (usually using Right padding).
I hope that helps.