I had the same problem with ignore all on one single document. All my other docs were fine. Here is how I fix the problem:

I first used the select all function, and copied the text I wanted to keep in the Word 2013 document I was having a problem with. I then opened Notepad and pasted the text to clear any formatting Word 2013 had made to the text. I then closed Word 2013.

After that I opened a new document up in Word 2013. Then I went back to the Notepad doc, and selected all, and copied the text. I then went back to the new document in Word 2103, and pasted in the raw text.

After I went through the document finding all the words Word was flagging, and did the "ignore all" option to all of them, and saved the new document. When I reopened the new document Word 2013 had remembered all the text I wanted it to ignore.

I hope this helps someone.
Seth