I would look at the support of you individual classes. If support for a given class is marginal in your fit model, the error may propagate in very undesirable ways. 

I would also consider fitting a series of binary models and predicting probabilities of each class separately. You could then perform a sensitivity test on the probabilities and evaluate if there is multiple pixel membership (eg., pine forest transitioning into mixed). 

You may be having issues with trying to validate a hard-boundary classification where fuzziness exists in the class margins. A probabilistic approach may allow you to evaluate the changes in the ecological gradients.

Random Forest to estimate land use in past with Landsat
I've just installed QGIS 2.6 Brighton using the OSGeo4W installation. The GRASS toolbox plugin has not, however installed as it had been with previous versions. Before, I was able to access the GRASS Tools via the tab Vector > GRASS, but it is now absent. Is this a change in the software or due to an error in the installation? If so, how can I rectify this issue?
