Weird graphics glitch

I've been using several tracks from the 2001 trackpack. Without any modifications made the starting lights on the gantry work for every track. However, when I alter the pitstands, muppets, garages and add/change the replay logo, on some tracks the starting lights on the gantry no longer work. Everything else is fine and the changes I've made all take effect, its just the starting lights that for some reason no longer work on particular tracks.

I've tried switching them with the lights from other tracks using GP4 Builder, adding the necessary tex files and updating the gp4 file and wad, but nothing seems to work. I'm sure it's something silly I'm missing but I'm kind of stumped right now.

Does anyone have any ideas?

Thanks.