Where do your 100mV come from and what exactly do you measure at the output pin? What is your measuring device? Scope? Multimeter?
Fact is that the PGA within the PSoC usually works fine, there are no known issues.
Can you draw a map Input Voltage versus Output Voltage
I made more tests and I discover that the real problem (apparently) was the Scope I was using. When I changed it everything worked very good! Now the PSoC works as lowpass filter!
Thanks for all help!