The maximum sampling rate with 1 channel enabled is 1GS/s corresponding to a 1ns sampling interval. With 2 channels enabled, the sampling rate drops to 2ns, and over 500ns this will give you 250 samples.
It appears that the data in your files may have been interpolated.
Are you using any other oscilloscopes?
Please could you download and try PicoScope 6.8.2 Beta from http://labs.picotech.com/
and see if this makes a difference.