I've recently just downloaded 2 textures packs, Vanilla Tweaks from xisumavoid.com/vanillatweaks and a customed texture pack from a Youtuber called fWhip. However I've had a few problems with synchronising both texture packs at once. The Vanilla Tweaks texture pack turns the rails into 3D blocks while the fWhip texture pack changes the colour of the rails. When combine the texture packs only result in one type of rail being 3D and texture which is the curved rail, while the straight rail, detector rail and powered rail are not. I've tried changed the order in the resource pack folder but nothing seems to work. I'd really apprecaite any support or comments and thanks for reading this.
OK so i had the exact same issue as you, it took me a bit to figure out but what you have to do in order for the 3D textures to work is go into Fwhips texture pack, go to assets and if your on windows search for "rail" and a lot of stuff should pop up delete all of it including the .png pictures and the .json files after doing this reload your texture packs in game and it should be working fine.
So to summarize delete everything in the texture pack relating to rails.