Could you please confirm the version of PicoScope 6 that you are now using?
Loading your data file into PicoScope 6.9.16, I can see that you have resolution enhancement enabled. If this is switched off (i.e. set back to 8-bits) the waveform appears again as per your pdf file.
Given that you have only 1000 samples collected in the waveform, and with resolution enhancement using a moving average filter, it is likely that the waveform is being averaged out.
You could try collecting more samples or another option would be to set the sin(x) interpolation on via the Sampling tab and reduce the sample threshold at which it activates via the Preferences dialog (accessible via the Tools -> Preferences menu).