Thank you for your post.
Where does this Excel file originate? I'm assuming it does not originate from Excel, because when you open and save it in Excel, the file imports correctly.
I did not even think of that, yes, it is being generated from our MIS system.
FileMaker Pro is somehow not recognizing the Excel file format your MIS system created. Your current workaround appears to work correctly. That is, open the file in Excel, don't make changes, save the file so that FileMaker can now recognize it.
I was having the same issue here: a generated excel file from our system did not import correctly in Filemaker Pro 11, the last column was also missing.
Opening the file in excel (or Open Office Calc in my case) and saving it without making any changes did solve the problem.
Somehow these automatically generated excel files seem to be missing something at the end...
Thanks for your post, it helped me a lot !