It would seem like the problem lies in the input file you made. I looked at it and the 3 output files you attached and noticed that the missing data was for block 1 (trials 1-40). Can you try the following and let me know if the data record correctly?
1) Create and run a new input file without block 1 in it.
2) Create and run a new input file without the first break (row 28 in the original).
Can you also send me a zip file with all of your original stimlists and any stimulus materials? I'd like to try running your experiment on my computer to see if I can replicate this error.
Jason Reed
Empirisoft Software Support Specialist