Time signal FFT different for whole signal than half signal on high frequencies
The primary issue is due to using a rectangular window with the floor being the result of spectral leakage. 

This is demonstrated in the plot below showing the frequency response (kernel) for the two rectangular windows used; one 500 samples long as red and the other 1000 samples long as blue. The corresponding rectangular window is effectively multiplied by your signal in time, thus convolves with your signal in frequency, resulting in spectral leakage as the spectrum given in the original question.  Thus you are seeing the smearing (convolution) of the actual spectrum with this kernal in each case. Using a window with a wider dynamic range (lower sidelobes) such as the Blackman  would result in a better view of the actual spectrum to the extent that spectral components now are getting buried under the spectral leakage. 



For further details on windowing and window choices, please see this post: Why would one use a Hann or Bartlett window?

You will also see a 3 dB difference between two windows if the signal energy is distributed wider than the resolution bandwidth in each case, since the resolution bandwidth for the rectangular window is $1/T$ where T is the length of your waveform. (So when you double the length from 500 to 1000, the resolution bandwidth is half resulting in half the power in each bin (unless a spectral tone occupies one bin in which case you would not see a change).