Oooookkkkkkaaaayyyyy....
This is getting annoying...
The mod which seemed to bug my game had been updated to NOT do so, as in have NPC mobs appear during the cart ride, this at first bugged the game and damaged some files or something as doing a File Integrity forced me to redownload them. The things that were happening were simple cart bugs and skips in the dialog. Now its just the dialog. Its not playing the Dragon Roars properly for some reason...
Uninstall the mod?
When it first caused problems I uninstalled it and had to redownload everything, when it said it fixed the intro bug it caused I tried it again...
ACTUALLY it seems that it wasn't the mod... Wait, checking integrity... EDIT 1:: Nope nothing missing...
Have an Idea on what other mod it could have been, been noticing more "Immersion" sounds from the mod "Sounds of Skyrim" it adds more environmental sounds. I don't think I tried a new game with it and its just been updated it could be accidentally overriding the Dragon's Roar from the intro...
EDIT2:: I started again, I got the roar. Then suddenly they chose to not push the stormcloak onto the chopping block. Gonna shutdown ALL my mods and see if its just Vanilla Skyrim thats fucking me over...