I was unsure if that could be part of it, so I moved the texture files into the base game folder.
Here are the options set under configuration. The textures are inside the base games directory.
http://www.ogier-editor.com/files_dod/Jackhammer_TextureOptions.jpg
This is what the texture browser looks like with the above configuration loaded. I notice that Jackhammer displays the textures by their specified name rather than path/filename.
http://www.ogier-editor.com/files_dod/Jackhammer_TextureBrowser.jpg
Here's a surface that should have the above texture (selected in the texture browser) applied to it. It instead displays as missing.
http://www.ogier-editor.com/files_dod/Jackhammer_TextureSurface.jpg
If I save this map, this is what is in the resulting file:
{
"classname" "worldspawn"
"gravity" "800"
"sounds" "1"
"mapversion" "220"
"_generator" "Jackhammer 1.1.700 (vpQuake2)"
{
( 512 0 256 ) ( 512 0 0 ) ( 512 -32 256 ) The Bricks [ 0 1 0 0 ] [ 0 0 -1 0 ] 0 1 1
( 256 -32 256 ) ( 256 -32 0 ) ( 256 0 256 ) The Bricks [ 0 1 0 0 ] [ 0 0 -1 0 ] 0 1 1
( 512 -32 256 ) ( 512 -32 0 ) ( 256 -32 256 ) The Bricks [ 1 0 0 0 ] [ 0 0 -1 0 ] 0 1 1
( 256 0 256 ) ( 256 0 0 ) ( 512 0 256 ) The Bricks [ 1 0 0 0 ] [ 0 0 -1 0 ] 0 1 1
( 256 0 0 ) ( 256 -32 0 ) ( 512 0 0 ) The Bricks [ 1 0 0 0 ] [ 0 -1 0 0 ] 0 1 1
( 512 -32 256 ) ( 256 -32 256 ) ( 512 0 256 ) The Bricks [ 1 0 0 0 ] [ 0 -1 0 0 ] 0 1 1
}
}
It seems to also be saving using the texture name rather than the file path/name. Would this be part of the issue?