An error is being logged, but nothing is being thrown, is it?
The code in question is:
Using java Syntax Highlighting
        // Now, recursively check that what it is based on is present
        boolean result1
;
        if (s.
getBasedOn()!=null) {
                String basedOn 
= s.
getBasedOn().
getVal();
                result1 
= activateStyle
( basedOn 
);
                
        } else if ( s.
getStyleId().
equals(defaultParagraphStyleId
)
                        || s.
getStyleId().
equals(defaultCharacterStyleId
) )
        {
                // stop condition
                result1 
= true;
        } else {
                
                log.
error("Expected " + s.
getStyleId() + " to have <w:basedOn ??");
                // Not properly activated
                result1 
= false;
        }
 Parsed in 0.012 seconds,  using 
GeSHi 1.0.8.4
 
  If the docx was created in Word, defaultCharacterStyleId should generally equal "DefaultParagraphFont", and this message shouldn't be logged.
How was the docx in question created?  What locale?
It'd be interesting if you could post a short sample docx exhibiting the issue (you can delete all content except for a bit of text, I would think).
cheers .. Jason