Hi mikegray! Sorry for necroposting, but you are not alone: for me "coc riverwood" also doesn't work when the game runs through SKSE64 - I also get a new game prompt. But "coc whiterun" works just fine.
For me "coc riverwood" also didn't work from the main menu - I got a prompt to start a new game (where I couldn't actually click anything). But "coc whiterun" works just fine.