This is because of the automatic rebinning, which combines datapoints to reduce dataset size and massively speed up calculation. This can be switched off in the GUI by setting the "target number of bins" (Data section) to 0. This is only recommended if you have really sharp features in your data.
Whilst this may be true, it is slightly misleading that under data points it reads a very small number which does not reflect the true file length. There is an additional column entitled 'Recommended number of bins' would it not be better to place this information there or have another column with 'Number of bins for analysis' as the title?