I've noticed the behaviour a couple of times, so not sure if it's a bug.
I regularly use comment boxes to instruct users what the workflow is doing, however after saving this file and re-opening come of the comment boxes have now moved in front of the tools.
Has anyone else experienced this and is there an easy fix?
I'm wondering if it's got anything to do with this idea by @johnemery and it's reverting to the default tool ordering in the xml?