Ive never seen this before? I compiled my map without any errors and everything seemed normal but when I try to run my map ingame, I get this error.

Fatal Error

Warning: couldn't open program files.wad

the warning there is VERY weird, the wording seems wrong in it... open up your .MAP file in notepad. double check what it has for the .wad locations

This part of the code, its right at the top.
"wad"
"\sierra\half-life\valve\halflife.wad;\sierra\half-life\valve\liquids.wad"

thanks.

I checked my map file and the main wad file I was using was not in the list. So I added it in, now should I compile again (I use batchcompiler) or what should I do?

if all the wads are now included in the right paths for hammer, then recompile it and see if it works ;)