MS4 and L3DT blended troubles

Just prior to MS4s release, I had an Atlas2 version of stronghold up and running. I had done this via unique terrain. After MS4, it no longer worked (even with the new lightmap settings in the .mis). Now I realize how much better a blended terrain looks, so I'm trying to recreate it that way. So far, neither method seems to work anymore. I hex looked over arcticBlended.atlas, and saw the l3dt texture directorie listed. I created a new, better placed texture dir, made a new climate with those textures, and ran the below commands. Hex checking the final output, I don't even see my textures listed, and needless to say it won't load.

// L3DT version
atlasOldGenerateChunkFileFromRaw16("client/data/terrains/l3dt/stronghold.RAW", 512, 4, 1.0/256.0, "client/data/terrains/geometry.chu", 2.0, 3);
importOldAtlasCHU("client/data/terrains/geometry.chu", "client/data/terrains/geometry.atlas");
atlasGenerateTextureTOCFromTiles(4, "client/data/terrains/l3dt/stronghold_opacity_Alpha1/Alpha1_x%dy%d.png", "client/data/terrains/opacity.atlas", 1);
atlasGenerateTextureTOCFromTiles(4, "client/data/terrains/l3dt/LM/stronghold_LM_x%dy%d.jpg", "client/data/terrains/lightmap_png.atlas", 0);
atlasConvertTextureTOC("client/data/terrains/lightmap_png.atlas", "client/data/terrains/lightmap.atlas", 0);
atlasGenerateBlenderTerrain("client/data/terrains/stronghold.atlas", "client/data/terrains/geometry.atlas", "client/data/terrains/opacity.atlas", "client/data/terrains/lightmap.atlas");

From the now ancient TDN article, I find some oddities.
First off, generate from tiles requires a 4th arg, which I'm assuming is 1/0 png/jpg. That at least output decent looking console messages.
This confuses me though:

Quote:
Note: The lightmap is the group of mosiac textures generated in the "Texture Map" process and the opacity map is the image generated in the "Light Map" process. Be careful to not get these confused.

The texturemap process outputs a unique texture, tiled or not. Whats in the LM dir is the actual lightmap. The opacity map with alphas et al is done via generate alphas. The example script (which my above script very closely follows) seems to do it the logical way, while the warning quote seems to completely contradict this.

So... my question is thus: WTF am I doing wrong? :) Perhaps the climate file and exact scripts used to make arcticBlended.atlas would shed some light on this, as that Atlas2 obviously loads and looks fine.