Nothing reproducible here (you parameters are not defined) and what the error might be is not shown. Best to provide a minimal working example if you want help.
This is the contour file contours1.txt (809.6 KB)
This is the one that I want to project on the shown profile. The columns that I intent to plot are the longitude (column 1), the latitude (column 2), depth (column 3) and the value of vP (column 5)
$point1[2] and $point1[1] (-C) are the initial longitude and latitude of my profile. In my case:
point1[2]= 68.5 and point1[1]=34. Same for the final point pairs (-E): point2[2]=39.0 and point2[1]= 70.0
So the x-coordinates looks OK and covers a good portion of your plot above, but the y-coordinate then given to psxy goes from 5.4 to 10.9 and that is why your pink circles are only at the top. From your plot it seems the expected y-range is 0 to 250 or so. Hence, your z-column is just not compatible with that 0-250 range. So there is no error going on here. The z-values are passed along (they are not projected as they are just data values, not coordinates), so I do not understand why you say this is an error when it in fact is an exact duplication of your input data column. Is there a unit issue, i.e., you need to scale your z-values to be compatible with your desired plot range?