The front page of the game warns that using save files from 0.18 on this version can cause bugs, that's why the update comes with prepackaged save files, so people don't have to start all over again. It's something that can't be helped unfortunately, RPGMaker simply doesn't like running older save files in newer versions. 0.20 and 0.21 will be able to run save files made in 0.19 though.