Hello,
I took your binary file, x_sine_adc0.bin and converted it to a text file.
The output shows what you have shown on the graph on the right.
However, this problem can be seen even if you were to load the first 1024 or 2048 samples and display it in the frequency domain - i.e. you simply get a blob of frequencies and the fundamental frequency will be incorrect. You can also try it on your end - look at the frequency plot of the large data acquisition file of, let's say, the first 2048 samples and the results are the same.
Our reference design (firmware) does I believe 16k sample acquisition and I have not seen this problem (if it shows up in 2048 samples, surely it'll show up in 16k samples). We also have the FMC Analyzer software that runs an acquisition of 8k samples 10 times a second and the frequency plot doesn't show the issue either.
I assume this is a custom firmware on your end that does the large data acquisition? Also, what version of the FMC150 are you using? Is it a DC coupled version?