Are you sure you clicked the "Mods" button? When adding a mod, you can select which mod to add but you cannot input any values. The values are already defined. Perhaps you clicked the "PermBoosts" button and thought it was the mods section?
In addition, the PermBoost section contains some values that don't work (I will remove these in a later release). One example that does work is Character -> Strength (or any other base attribute).
If this still does not work, I can try this scenario myself, but I don't see why it would fail.
Ok so my steps again, after your advice,
1. Open my save via medit alpha 9
2. Select Roderick
3. Select training sword having moved it to my inventory before saving in game.
4. Select a small dmg boost mod and a leadership mod.
5. Select str perm boost with a modifier of 2
6. Hit apply, then save the save.
7. No changes once I load in game. EXCEPT I can change it's type from common to magic, that shows. Neither the perm boosts or mods are applying.