I seem to have the same issue as Automatic Weights Different on one side than the other which doesn't seem to have a solution.
I've tried removing and reapplying the automatic weights on both sides and consistently the Right (mirrored) side doesn't add the weights properly while the Left (original) side does.
Is there a solution to this bug yet? (assuming that it is a bug of some sort) I'm using 2.79, I think it has something to do with the mirroring process or the bone roll but I really can't say for sure.
If i have to manually assign weights to the meshes is there any way to make the them act the same on both sides?