Hi Elana,
Under the ToBI standard each non-silent word should have a break index associated with the degree of disjuncture at the end of the word. It may be an issue where the way that silent words are marked in the file you're working with are not recognized by AuToBI. Words that match the regular expression: (#|>brth|brth|}sil|endsil|sil|_|_\*_|\*_|_\*) will be considered silent. you can change this regular expression using the command line flat -silence_regex
About the results this is valid output, though most likely very incorrect. The accent/deaccent decisions are typically reliable, the accent type predictions, however, are quite errorful. (They're still state of the art, but it's a challenging task. I'm still trying to figure out the best way to handle this -- some people have reduced the task to HIGH/DOWNSTEP/LOW distinction.)
-Andrew