The prices shown in Uridium may not be reduced to reflect the rebate when displayed - but there should be an adjustment made after purchase to compensate (you can check this for yourself on the Balance page of the URIDIUM section). If you believe that there has been an error of any kind with your Uridium balance, you will need to direct any questions to Support, and they can assist you.
For the shields problem, it is difficult to answer without more details. The only advice I can give, is that you may not notice a significant increase until you have upgraded by quite a few levels. A 1% increase to the shieldpower of one generator does not equal a big increase overall, but after you have several drones/shields fully upgraded, you will definitely notice the difference.
Do you have further questions?