Are you rendering it before you view it (when the transitions are not showing up)? If you haven't rendered it monitor playback could be jerky and skipping and not showing new bits you have done to your project.
What are your system specs? CPU and RAM need to be pretty good to cope with longer, more complex projects. Premiere is a known system resource hog - I use the Premiere Elements version and it will slow down incredibly when adding multiple effects, on projects with multiple tracks etc. I have to render each little bit I add sometimes so that I can see it properly flowing in the monitor. CPU usage sits at around 95-100% when doing complex things.
