OKay, after a few days of testing, I have traced the issue to some kind of interaction between Cubase 7, Automap and the Sonnox Elite Bundle of plugins.
I rolled my pc back to the point before I uninstalled Automap. With Automap on again, the songs are loading. By unticking my plugins one at a time in the Automap server, and then loading one of the songs in question, I found that whenever one of the Sonnox plugins were not under Automap control, the song would not load.
It looks like Cubase is having trouble loading a preset into an 'unwrapped' Sonnox plugin that was saved within a 'wrapped' version of the plugin. Not sure if it's a Steinberg, Novation or Sonnox issue.
If any other peeps out there are using the Sonnox plugins I'd be curious to know if you can replicate this.
1) Create a blank Cubase 7 song with Automap on. Add one audio track. Insert an Automapped Sonnox plugin.
2) Make some random settings on the Sonnox and save it as a preset, using the Sonnox onboard preset manager buttons.
3) Quit the song. Quit Cubase.
4) Go into the Automap server and 'untick' that Sonnox plugin from Automap control.
5) Relaunch Cubase and open the song again. Does it load, or does Cubase have "a serious problem".
Cheers.