I posted a similar message a few months ago for pretty much the same reason.
A bunch of people told me it was illegal, but no one cited a specific code section.
My belief is that the two cables must be run together, with the same staples, through the same holes, etc. As long as you do that I can't see why it would matter that the conductors are not all under the same jacket. The only code I could find was that all conductors must be together in the same raceway when metal is encountered, but that does not seem to be a problem.
Now... an house inspector might take exception to it when you go to sell the house, but unless he can cite a specific code violation...