I'm with Faré on this one. I don't see evidence that this change is
because ASDF is doing something bad. I believe it's consistent with the
hypothesis that there was some imperfectly-controlled aspect of building
that is done differently now (e.g., files loaded in a different order
where both orders are compatible with the constraints in the system
definitions).
This doesn't even look like an ASDF error to me -- it looks like an
error that occurred while loading a system that ASDF has re-packaged.
So we might be able to help you debug this, but without more evidence,
there's no reason to believe that ASDF has done anything to you: it
looks like the change in ASDF just reveals a pre-existing bug.