Looks like you are using some 060 turnouts as well as 036/031. With Fastrack, the 060 and 072 turnouts include 1/3/8" "makeup" straight. RRT requires the use of those to auto connect to the next track. The makeup straight (road bed missing from one side) compensates for the design of the 060/072 switch. This will create the need for adjustments in your design. Use the PDF for Fastrack length combinations. I have found that what does not line up in RRT sometimes has enough "give" with that the actual track will connect and not effect operation of your trains.