Trying to debug this now and the problem seems to be in components/com_fabrik/models/form.php @ function processToDB.
I am comparing what happens in this function when updating a row with what happens when you import a CSV.
I haven't quite tracked down the problem yet, but I wanted to comment on how this function stores its data. At entry, formData holds a variety of properties, including all placeholders with ___. With the table___element format, each of these is likely to be unique and unlikely to conflict with any other properties stored in formData. However...
It then runs $listModel->removeTableNameFromSaveData to remove the table name and ___ and just leave the field names. This is fine so long as the shortened names are a. unique within the elements being saved (which might not be true) and b. don't conflict with any other properties used by fabrik. But I can easily see how these might NOT be unique. Indeed with common field names such as id it is quite likely for there to be a conflict.
I would recommend that:
1. The removeTableNameFromSaveData returns only placeholders.
2. The returned values are stored separately for each table and separate from other fabrik formData.
I will update this further once I have fully tracked down the problem and submitted a fix PR.