The issue of reconciling tropical temperature trends at the sfc and in the troposphere rumbles on, although in a not very serious way: its a good subject for research, but it doesn't seem to be a major septic playing point, probably because the issue is too complex to get much traction.
A brief recap: once upon a time the satellites said the trop, globally, wasn't warming. That disappeared ages ago. We're now looking only at the tropics, which are warming too, and the remaining issue is whether the trop warming is compatible with the surface warming. Models and (we believe) basic physics says the trop T mid-height should warm about 1.4 times as much as the surface. Everyone agrees that for changes like the seasonal cycle, this is true. The issue is whether its true for the long-term trend.
Enter "A comparison of tropical temperature trends with model predictions" by David H. Douglass John R. Christy Benjamin D. Pearsona and S. Fred Singer" in press in IJC; and "Tropical vertical temperature trends: A real discrepancy?" by P. W. Thorne, D. E. Parker, B. D. Santer, M. P. McCarthy, D. M. H. Sexton, M. J. Webb, J. M. Murphy, M. Collins, H. A. Titchner,1 and G. S. Jones; GRL VOL. 34, L16702, doi:10.1029/2007GL029875, 2007.
You don't have to go far to see that Thorne et al is a higher quality paper. The basic conclusion is that the uncertainty in the trends from the satellites is large enough that there is no inconsistency.
Weirdly enough, Singer et al come to the opposite conclusion: that they are inconsistent. I doubt very much whether their error analysis is good enough to conclude this. One problem is that they lump all the IPCC runs together, without noticing that some are rubbish (though to be fair the IPCC does this too). There are clearly errors in the review copy: model 17 has a trend, in unspecified units, of 219 at the sfc at -1275 at 1000 hPa; they should be very nearly the same (model 2 has a simlar problem. Curious. Singer et al very late on remove these "outliers"). The uncertainty in the modelled trends is taken to be the inter-model SD/sqrt(n-1), which I think is dodgy. And table III invites us to believe that the obs have no uncertainty, which is tricky, since they disagree amongst themselves.