Man, I had the same trouble and I JUST found out what was going on (I think). I'm building a mine from scratch, so I did as the tut suggested and copied the aaamarkers cell (or whatever it's called). I'm a fan of Realistic Lighting, so the first thing I did was remove all ambient light from the cell. Since I worked with 'A' toggled, I didn't notice the light problem until I tested it.
After much beating of my head against the wall, I just Cell window cell - > Edit - > Lighting and set a Template (BleakFallsBarrowClose). Then I set the fog color to black and the Directional color to black, went to the Directional Ambient Lighting Tab and just clicked on the Set From Ambient button. Saved, checked in-game, worked great.
Except - now I had lots of ambient lighting. Urgh. So I went back and set my ambient to 39/34/22 (RGB) and set the directional from it. Still too much. So I went back to the Directional Ambient Lighting tab and set the Z colors to black. Went in-game, pretty daggum dark, the lights work good. So I set the Y colors to black. Darker still, lights still work. So I set the X colors to black.
And found the problem. Apparently, there has to be some kind of ambient light for the torches not to pop in and out. I dunno why, maybe there is something else. But with just a touch of ambient, the lights work fine. With my Ambient set so low, it's nearly pitch black - you can only see something you're looking directly at up close. So that's okay.
Maybe one of the Realistic Lighting folks can pop in and answer this one better. I hate to just 'get things working' without knowing what's going on.