The topic of ion interactions with membranes is complicated since in the model it depends on both ion and lipid parameters. There are probably inaccuracies in both of these.
I think that the ion issue discussed in the manuscript could be divided into two different problems:
1) the partitioning of sodium ions is probably too high and
2) the membrane response to the ion partition is wrong.
It could be that the first issue is solely related to the ion force field and the second issue to the lipid force field, however also cross-relation is possible. For example, it could be that the Sodium partitioning is too high because membrane response has too low energy cost. Several other scenarios are also possible.
There is at least one thing which could be assessed to clarify the issue: The electronic polarizability. Recently, it has been suggested that this could be partially taken into account by scaling the charges [Leontyev et al. PCCP 13, 2613 (2011)]. It would be interesting to try out if this approach would improve the partitioning issue (1). I do not believe, however, that the membrane response issue (2) could be fixed simply by this approach; there is, namely, a problem in the membrane energies in all the other cases as well.