What you need to do in order to force it to download 3.1.3 is:
1. Launch Tekkit
2. Click on 'Options'
3. Tick the 'Manual Selection' box - the dropdown becomes active
4. Scroll up the list until you find '3.1.3 | 1.2.5 | Latest
Hope this helps!
EDIT:
Hang on hang on hang on, it doesn't appear at all, not even if you scroll all the way up? It's normally just about hidden in the list (it shows 3.1.2 and under and just misses out 3.1.3 until you scroll up)