I have played many strat 1v1 multi-day auto games and they have all given me a 100% multiplier; I don't see what's wrong.
The only other reason you would be receiving diminished points is because you may have played the person recently. (Level 8+ only) In that case you would receive half of the points you would normally receive. If you beat them three times or more, then you receive 80% less points than usual. This means...
If you played a real-time game with changed killrates, used ad-blocker without having a membership, were at level 8 or higher, and beat a level 1 person that you have beaten at least 3 times in the past 10 days, you would only get 2 points.
Honestly I think you should check http://warlight.net/Points
- it details how many points you got and why you got those points.