Sometimes when I open up several of my projects I get a warning that says:

"The line endings in the following file are not consistent. Do you want to normalize the line endings"

I click Yes (defaults to Windows CR LF) & proceed to work on the program. Then I might open it up several days later & get the same warning.
What causes line endings to become inconsistent in the first place & why don't they stick when I say yes to normalize them?