I have an SD-9 Commemorative diesel that has round head screws holding on the side frame assembly, and they do indeed rub on a traditional Flyer re-railer. The re-railer has a slight ramp towards the middle of the "crossing" and slightly lifts the truck from the rails. Is that what happens? Do the engines simply stop, or do they refuse to move when pushed? The sprung sliding shoes should keep in contact with the rails, though. Looking at the side frame center, it looks like the SD-9's have a slight counter sink like the Gilbert ones, so a flat head screw may just be the cure. I have a number of EP-5's that have flat head screws in the same location like the Gilbert ones, and they pass over the re-railer just fine. Be sure the threads are compatible, though.
BTW, I run SHS track and set up a few sections of Flyer track to test it out. Good luck!
