In case you haven't noticed, a patch is now available in the File Library to address problems related to the creation of procedural turnouts in the "abandoned" track type, such as is found in the Johnsson Gravel spur. Here's the link...
http://railworksamerica.com/index.php/download-library/rw-a-addons?view=document&id=3358:rw-a-lakeside-abandoned-track&catid=30:rwa-lakeside-addons