SmartPlaylist relies completely on the MediaLibrary present on the device and has not been adapted to iTunes Match, if this is possible at all. Other developers are also struggling with this.
Accessing a song up in the cloud (iTunes Match) seems to change something in the MediaLibrary. Unfortunately I cannot distinguish between these Match-changes and real library changes after synching. Maybe I just have to ignore changes and people have to restart SmartPlaylist after synching, like before. Alas, Apple does not make it easy.