the export of the submissions is simply a csv dump of the results table, where the columns have been re-ordered according to the current position of the fields. The structure of this results table may become messy over time when you create, delete and move fields. There may be columns left over from fields which have already been deleted, and if you have upgraded just recently, there may even be columns missing for fields that were added after the first submission.
In recent versions of mpform you can clean that up quite easily: Just open the general settings, and save them again, without changing anything. By doing so, the missing columns should be re-created.
Obsolete columns however are not removed. If you want to do that, you can change the results table suffix. Old submissions however are not moved to a new table with that suffix, but this would be an easy way to start from a fresh table for future submissions.
Please let me know if these steps helped you to clean up the mess that you have described. If the "mess" persists, do you see a chance that you can create an sql dump of your mpform tables and share them with me (preferably by email) so that I can have a look what exactly is causing the trouble in your case?