Curved noise floor and ugly unexplained peaks after FFT
Does the 'same configuration of your analyzer' mean the 'same sampling rate'? Is that equal to 41 MHz? It looks like you faced a well-known problem with a Nyquist criterion practical implementation. I mean that some time ago in digital oscilloscope ads there was an exact Nyquist ratio between a sampling rate and channel bandwidth (especially for cheap ones). Now it is about 10. (You may want to look at any ads of digital oscilloscopes) I remember there were several articles with figures similar to those posted here. To check this hypothesis just check a sampling rate of your spectrum analyzer (you wrote that artificial pikes are not seen in a spectrum analyzer with the same configuration.) or try to use a higher sampling rate in your data processing procedure if possible. In order to get at least an intuitive idea of the reason lies in the foundation of the problem perhaps you want to check this: Why is it a bad idea to filter by zeroing out FFT bins? 
I suppose the following paragraph from the cited answer works for you: 'So if your original FFT input data is a window on any data that is somewhat non-periodic in that window (e.g. most non-synchronously sampled "real world" signals), then those particular artefacts will be produced' This phenomenon is called resolution bias error, or more commonly, the picket fence effect http://www.azimadli.com/vibman/thepicketfenceeffect.htm. Here you can find an illustration http://www.mechanicalvibration.com/More_on_spectral_leakge.html