When normal.dot os corrupted, there tends to be lots of odd things happen with formats inside documents, as you describe.
The cure is to delete (or rename) normal.dot. Word will reconstitute it when Word is started again.
Ifind it better not to try and change normal.dot, but to make a template how I like, then save it as "mynormal.dot" and use that one. Tends to cause less issues with old docs created with the standard normal.dot.
"Save and close the document" - You don't do that to make a template - you must Save As - and choose file type Template (.dot) for it.