Are you sure it's your gun damage? elemental damage is always applied first, if enemy is already killed by elemental damage then the gun damage itself won't appear.
Don't forget it does half damage to light infested. Just in case you've changed opponent type (has caught me out before with AP damage weapons).
Not too sure anymore since the Dead Eye aura mod is in works (it was released early accidentaly, and propably being revisioned). Whether this replaces Rifle Amp's place in giving sniper rifles extra damage as an aura, is yet to be seen.
In my personal opinion, I do believe it will.
I can guess two obvious options:
1. You're trying to fignt against light infested - they're halving the damage
2. You're using split chamber and damage dealing with a first bullet is enough to kill a target - that's why multishot does not proc.
Rifle Amp doesn't work with Vectis, sillies, Dead Eye is what you should be using
-too lazy to log on, Hysterical Tenno