You want a case where molecular results keep finding phylogenies that
are not well agreed upon, simply look at the _Gavialis_ - _Tomistoma_
back and forths. Molecular phylogenies routinely found a sister group
relationship of _Tomistoma_ and _Gavialis_ in a sister group to
Crocodylidae, while morphological results split them off with
_Tomistoma_ being a crocodylid and _Gavialis_ being a basal
crocodylian.
Also, I'm curious as to what papers you and David Marjanovic have
been reading in regards to squamate phylogeny. The (or one of the)
most recent phylogenies to come out using a "total evidence" approach
found monophyly among amphisbaenians (Wiens et al. 2010). This
supports the morphological data, but goes against what the molecular
data has said (Townsend 2002, Townsend et al. 2004).
According to the authors:
"...although our main focus is the impact of molecular data on fossil
taxa, we also show that addition of morphological data can change the
placement of living taxa relative to analyses of molecular data
alone. In our study, the molecular data alone (15,794 characters)
show strong support for nonmonophyly of amphisbaenians (i.e.,
Rhineura outside amphisbaenians) in both parsimony and Bayesian
analyses (bs = 98%; Pp = 1.00), possibly due to long-branch
attraction. Yet, monophyly of amphisbaenians is strongly supported
when the 363 morphological characters are added in both analyses (bs
= 83%; Pp = 1.00)."
The authors found here, and previously (Wiens 2005) that despite the
small number of morphological characters relative to molecular data,
these phenotypic data carry much greater "weight' in analyses than
the molecules.