I've noticed the same causes and correlation. Canker sores' formal name is aphthous stomatitis. But whether it is an autoimmune disease is debatable. As noted in [1]:
"Despite this preferred theory of immuno-dysregulation held by most researchers,[7] aphthous stomatitis behaves dissimilarly to autoimmune diseases in many regards. "
"Despite this preferred theory of immuno-dysregulation held by most researchers,[7] aphthous stomatitis behaves dissimilarly to autoimmune diseases in many regards. "
[1]: http://en.wikipedia.org/wiki/Aphthous_stomatitis