All the excel sheets that I am working with through the last year where I have imported data into them from txt/csv (even when is just a column of numbers), I have had to go through the following error messengers every time I open them(!):

"Excel could not open filename because some content is unreadable. Do you want to open and repair this workbook? If Excel cannot repair the file, some data may be lost."
"Excel repaired or removed unreadable content from this workbook. Do you want to review or save the loge file?"

The log file looks as the following:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<recoveryLog xmlns=""><logFileName>Repair Result to filename 08987.xml</logFileName><summary>Errors were detected in file 'Macintosh HD:Users:C:data:filename.xlsm'</summary><repairedRecords summary="Following is a list of repairs:"><repairedRecord>Repaired Records: External formula reference from /xl/connections.xml (Data connection)</repairedRecord></repairedRecords></recoveryLog>

After all this my workbook opens and nothing is changed. On top of the table there is a yellow bar with: "Security Warning Data connections have been disabled."
and the possibility of me Enable Content. And the filename on top of the window is now shown as filename.xlsm [Repaired]

I can enable it the content or close the warning, but it has no effect.
If I save the file (also under a new name or with xlsx or xlsm) and opens it again, I go through everything again. I have also tried to delete the columns that I have imported, but the problems doesn't go away even with that.

The problem seems to be my Data Connections. Which I assume is the connection to the original text files.
After I have imported text file, I don't need there to be any connection to the original text files, and I often delete the text files afterwards. But how to get Excel to understand that. I have just found a rough solution, where I can import the data into one workbook and then copy it over to my real workbook, and pasting it special, clicking values. Which seems to get rid of the original data connections. But most of my excel workbooks are giant and too complicated to do this now, as it would ruin all the formulas.

Do anyone know how I can solve this problem long term?

I have seen a few other people with mac excel 2011 writing about similar problems, but I have yet to find someone who found a solution.