bobbyd has a good question - are you using a 1008 relay to power isolated rails on the crossing?
If yes - then the relay may not be wired correctly or not functioning correctly. If you have a 1008 connected first pull the red led light from the 1000 switch motor and see if things are functioning. There was a bad batch of leds on some DZ-1000's that affected the performance of any relay connected to the 1000. if this does not fix the problem then you may have a wiring issue.
If no then you may need the 1008 to power the isolated rails on the crossing.