First thing I always suggest is to clear your data folder and see if the same thing happens. Ok, actually, the first thing I always suggest is to read the data FAQ here: http://www.empirisoft.com/medialab/help/data_faq.htm

But it sounds like you have done that. In that case, let's troubleshoot. First, off can you get this result if you run the questionnaire alone (i.e., without running it through an experiment file)? If so, please send me or post a copy of the .que file. I'll try running it here and see if I can replicate the result--if I can, then I can probably figure out what's causing the missing values.