Hi Jordan,
I'm glad you managed to track down the responses. It seems like all the data has been written correctly, and the issue is just to do with the parsing of the file into .csv format. Usually when I have encountered problems like this, it is due to participants putting odd open-ended responses, but this does not seem like a plausible explanation in the current case.
Everything is correct in the byvariable file, right? Do you get the same issue with the .sav versions of the files?
Thanks,
Joe Simons