Hello Itay,
I was trying to recreate your issue here by having both the actual signal coming from my DAQ board and the Simulate signal on the same program. I also used the function Power Spectrum.vi for the power spectrum analysis (Are you using this function too?) I sampled both sine waves with a sample rate of 10KHz, 1000 samples to be read and a frequency of 100 Hz.
With this configuration, I got two spikes (one around 0 and the other one around 1000) and an amplitude of approximately 0.25 for both. Both results (using the Simulate Signal Express VI and the signal coming into my DAQ board) were similar to each other which makes me believe its working.
Something to pay attention at is to put the Convert from Dynamic function before wiring the
incoming signal into the power spectrum function (Do you have that function in your VI?) You can find this function by clicking on search and typing the name of this function (What version of LabVIEW are you using by the way?)
If this didn't help, please indicate me all the frequencies you are using (the sampling rate, the number of samples and the frequency of the signal)and the amplitude of the signal, and what you are expected to see in the Frequency domain (what amplitude and frequency spikes you are supposed to see) so that I can recreate exactly what you are doing. Attached you will find the VI I built using LV 7.1 and a screenshot of what I am seeing.
Thanks,