What Is the reason behind it? Please Explain.
In your 2nd circuit, you have grounded R1 to the negative power rail of the op-amp after removing C3. This creates a massive DC offset problem and, the circuit won't properly amplify signals. If you look at the 2nd graph in detail that's what you see; the gain is \$50\times 10^{-9}\$ at 2 kHz and zero at DC. This tells you there's a screw up in your circuit (which I identified above). Gain of 50.0 nano: -

If you want to fix this use two resistors of value 2 kΩ replacing R1 with one tied to 3.3 volts and the other tied to ground: -

Or connect R1 to VCC/2.
Signal Without Capacitor (C3)
It's not a signal it's a gain. A signal would be that seen using a transient analysis. Effectively, what you have is a bode plot. I would also recommend that use use logarithmic scales for frequency and dB scales for gain.