Transition state and intermediate very close to each other I've been studying a particular reaction with DFT, where a transition state and the following intermediate are very close to each other. The change in geometry is rather small and therefore the electronic energies differ only by about ~ 1-2 millihartrees. Still, the TS has the higher electronic energy (everything else would be surprising?), but adding thermal corrections to both structures leaves the intermediate about 2 kJ/mol higher in energy.

Does that make sense? Or is there something I did not consider in my calculations?
1 Kcal/mol is indeed quite low. This is around 1 hydrogen bond energy. In general - compute frequencies using freq command in Gaussian or whatever you are using. You should have a single negative frequency. It should be relatively low (abs value compared to lowest positive frequencies). Visualize it using Moleken or a similar tool. If movement is along the reaction coordinate then you are good.

Also, compare all bond lengths and angles to see what changed. Did bonds along the reaction coordinate change the most?

Please use Kcal/mol instead of Hartrees. I realize that Gaussian prints out 
Hartrees, but it is easy enough to convert to Kcal/mol.