I have the similar problem,too!
[I][edited by moderator][/I]
I'm using MediaLab v.2004 and I'm having similar problem of missing data. My .exp file have four conditions(4 different orders of the questionnairs), and in each condition there are 6 questionnaires in the fixed order, finally in each questionnaire there are 100 items (random order) in four blocks (fixed order of block).
But when I run my experiment at any one of the four conditions, some time the program just could not finish all the items in one questionnaire (random questionnaire, but not a specific one every time), and then the rest of the items in that questionnaire were skipped which were recorded as 99 default number in the data file. I could not figure what the problem is, since it happens randomly by questionnaire and randomly started to skip from a item. Some time, the program went pretty well, but some other times the data was just missing. Thank you so much.