Without the data file it is almost impossible to see what is causing the problem.
Try importing the file and then doing
ListPlot3D[Take[data2[[All,{1,2,3}]],20]]
That will extract the first 20 points of your data and plot only those. Does that work? If so then change the 20 to 40 and see if that works. If that works then change the 40 to 100 and see if that works. If 100 works then try 1000. You are trying to test if some part of the list of points does plot and more points do not.
If you can estimate where the data points do not plot then you may be able to look very closely at the data and see anything that is not simple data points much like other data points near them.
Your notebook showed a small sample of your data points and I was able to cut and paste those and that plotted for me.
If this does not work for you then perhaps attaching your data file to your post might let someone else look at the data and find the problem.
