I used to use one of these (cant remember) to find leaks before i had to reformat. Now that i installed an updated hammer, the .pts or .lin files dont appear in the 3D view like they used to and i cant use them to find the leaks anymore. Can anyone help me here?

Download Hammer 3.5 beta. A quick google should get you to it.

http://collective.valve-erc.com/index.php?go=hammer_beta

its a new feature of beta 3.5 , seeing the pointfile in the hammer editor.
use the .lin its a "shortened" more linear version of the .pts .