The paper Atyy linked to touches upong the question I asked surprised about.
"
Any quantum theory of gravity which attempts to deal with the landscape
of string vacua by constructing different vacua as solutions of a
single theory in terms of a single set of degrees of freedom will face
this field-redefinition problem in the worst possible way. Generally,
the
degrees of freedom of one vacuum (or metastable vacuum) will be defined
in terms of the degrees of freedom natural to another vacuum
(or metastable vacuum) through an extremely complicated, generically
quantum, field redefinition of this type. This presents a huge obstacle
to achieving a full understanding of quantum cosmology. This obstacle
is very concrete in the case of string field theory, where it will make it
difficult to describe the landscape of string vacua in the language of a
common theory.
It is also, however a major obstacle for any other attempt
to construct a background-independent formulation of quantum
gravity (such as loop quantum gravity or other approaches reviewed in
this book). Only the future will tell what the best means of grappling
with this problem may be, or if in fact this is the right problem to pose.
Perhaps there is some radical insight not yet articulated which will make
it clear that we are asking the wrong questions, or posing these questions
in the wrong way."
--
http://arxiv.org/abs/hep-th/0605202
I think a clue here is to see that the core of this problem is not specific to a particular program. It just tends to "show up" in different ways. And maybe it alone suggest that we need a new way of thinking of what a theory is. Should we think of theories as descriptions of reality, that are either wrong or corroborated, or should we think of theories as interaction tools?
ie
isn't the situation here suggesting something much worse than just mathematical difficulties? If it is that we simply are conceptually confused about certain things here, it's not a mathematical problem. One problem seems to shave out and separate conceptuallt unclear questions from technical problems of conceptually clear questions.
/Fredrik