Is it just the transitions that are out of synch? With you saying the whole thing is out of synch and then mentioning the transitions, I wasn't quite sure whether you just meant the transitions between your three edited clips or the audio and video of the "published work" as well as the transitions were all out of synch.
Have you worked with Movie Maker before and had any trouble previously? I only ask because the final rendering or publishing of a video is very demanding of a pc and normally even before working on video you need a reasonable amount of ram and free hard drive space and an uncluttered pc, that means defragging and stopping uneeded programs running, all them icons in the notification area by the clock, see if they can be turned off, some people even switch their routers off and turn off the anti-virus while video editing.
Have you still got the project file for the work, I normally save the project as a MSWMM file before rendering it, so if anything goes wrong during the rendering providing the original footage is still on the pc and in the same location it can be reworked on.
If it's just transitions out of place the original project file can be opened and viewed in Time Line view not Story Board view, in Time Line view you can remove transitions in the transitions pane.
If you haven't got a project file and it was just the transitions out you could perhaps open the rendered file in Movie Maker and cut out the parts you want to work on and insert cuts to replace them parts from the original footage and insert transitions again.
If everythings out of synch audio/video the audio may be able to be nudged into synch. From my own experience it sounds like the pc was struggling during the rendering, in which case it may be better to do the editing, save the project file, switch the pc off for a while, then switch on again and then do the rendering/publishing.