I posted in another thread somewhere about this same issue....
first, count the teeth on the spur gear to ensure it is the correct spur gear for the ratio that you are trying to get there have been some miss labeled.
I have only had 1 synergy model of mine that the mesh was perfect on the large to small spur gear transfer. I have had to use a small jewelers file to open the transmission holes up a tad on the rest. it doesn't take much, only about 4-5 passes back and forth with the file, so don't take too much off!!! its easy to do!!! also, be very sure to keep in a straight line, and don't get your holes off true.