There are many things that can score 1000 points:
Bow and Arrow 1000 point relay (resized).jpg
So determining which part of the circuit might have an issue is hard to say. Can you be a little more specific about when the problem happens?
I assume that it happens when one of the multiple 1000 point awards is happening. The multiple 1000 point awards are driven by different Score Motor Switches (in the circles in the schematic above). It may be that one or more of those switches isn't closing reliably or long enough to advance the Score Reel. If you can narrow down when the problem happens, or when it doesn't happen, that might help zero in on the likely switch(es).
The motor chart below the schematic shows when each of the switches closes as the motor turns. A switch on motor cam 2 for example closes 5 times as the motor turns through one cycle while a switch on cam 3 closes only once. The chart shows two complete Score Motor cycles.
/Mark