I recently went through the same thing and did exactly as you did. Downloaded Coker's Smashword's Style Guide, started to read it and like 10 pages in I was like screw this I'll just compile in Scrivener for .doc. What could possibly go wrong? Well, it passed the meatgrinder (somehow) so I downloaded my book from Smashwords to make sure it converted right to the different formats and it looked terrible. Font was like size 20 and indentations were screwed across the board. I immediately unpublished and now I'm going through the painstaking process of RTFM'ing (which I should've done in the first place but at least no harm no foul; it was taken down before anyone saw it). I recommend you do the same.