It sounds like you're forgetting an important step. That is, after replacing the .data and mission files, you must delete the FDList file. If you skip/forget this, you're staying in this loop forever!
Navigate to C:\Program Files\SD EnterNET\ENFUNS Updater\Downloaded\NAVYFIELDUS and delete the file: FDList.
If you're still having problems, do the repair thru the automated installer in this thread:
http://navyfield.com/Community/Forum/View.aspx?num=3499&searchtype=0&pagecount=0&searchvalue=&sort=5&category=E01&page1=1
Phrozen
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