"The index is out of range" error messages

We have been running several batch Prepare tasks from new projects on a source folder containing about 40 files or more using Trados 2007 TTX files as reference. Each time, an error is returned for a few files, but the files generating the error are not always the same. The error details always start with "<SDLErrorDetails time="24/01/2014 13:33:30"><ErrorMessage>Index hors limites (#). Le nombre doit être compris entre 0 et le nombre d'éléments dans l'ensemble (#).". (In English: The index is out of range...). The number indicated in parentheses changes for each file.

When we open the files that have generated errors, we notice that no segment is translated. The 100% matches will be populated automatically as we start translating the file. For the fuzzy matches, we'll see the concordance search results in the upper pane, some as good as 99%, but the Select Previous Match, Select Next Match, and Apply Translation are all disabled and greyed out. The only way to apply a translation is to manually copy from the concordance results and paste it into the target pane.

What can we do to prevent these errors from happening?