I agree with Mark on scrutinizing score switches.
My advice, be thorough.
Run a point file, not a flexstone, mildly across each point. If you are comfortable with Nic's dremel method then go for that approach. Wipe the debris out after filing with a qtip dipped in alcohol.
Then inspect each switch manually for wipe.
Going through the complete score motor, if you have the main relay board out of the game, only takes 20 minutes or so. When in the game it is more difficult and will take longer. You may find going through the few switches thoroughly is all you need.
One last thing. If this has been covered I apologize for repeating. While it is quite uncommon, check the switch dog positions for L(long) and S(short). The switch dog is the tab that contacts the switch stack at each cam position. If someone before you has put them in the wrong place it can cause these type timing issues. Where the position is engineered is listed on the schematic at the score motor diagram.