Thanks for the reply.
With further testing it looks like the issue only occurs with loops, quark screws, and those types of sections in the track. Unfortunately, adding more gizmos does not alter the broken sections. They just stay broken and it becomes very difficult to manage those areas. The fix I have found, although not ideal, is to break up those splines into several pieces and then apply a copy of the railclone to those splines and apply separate RCSpline mods to them. That way I get the results I want.
Hopefully future revisions will resolve this issue.