Hi Hiltk,
Based on your description, you said when you type period button, the update table of contents popup. Could you tell me if this issue appeared in all files or only particular file? And you said you check the shortcut in Word. Could you tell how did you check the shortcut in Word?
In Word, you could custom keyboard shortcuts of features. Please check again with these steps.
File-Options-Customize Ribbon-Keyboard Shortcuts: Customize
Then you could get the dialog box as shown in the following figure.
Now make sure the drop list of Save changes in, all of the files did custom keyboard shortcut, the content of Current keys are empty.
If this issue still exists, I suggest you recreate a Normal.dotm file for Word.
Normal.dotm is the template upon which all new blank documents are based. It opens whenever you start Microsoft Office Word 2013 and it includes default styles and customizations that control the basic look of your document. Changes you make to Normal.dotm will be applied to documents that you create in the future.
The path of Normal.dotm:
C:\Users\username\AppData\Roaming\Microsoft\Templates
Please dont delete this file, you could rename it as Normal.dotm.old. Then you reopen a new document, Word will recreate the file in its original default location. After recreating this file reset all changes you have made to the Normal template.
Then check if it works fine, after this method.
Hope its helpful.
Regards,
George ZhaoTechNet Community Support