The standard paradigm in Affective Computing involves acquiring one/several markers (e.g., physiological signals) of emotions and training models on these to predict emotions. However, due to the internal nature of emotions, labelling/annotation of emotional experience is done manually by humans using specially developed annotation tools. To effectively exploit the resulting subjective annotations for developing affective systems, their quality needs to be assessed. This entails, (i) evaluating the variations in annotations, across different subjects and emotional stimuli, to detect spurious/unexpected patterns; and (ii) developing strategies to effectively combine these subjective annotations into a ground truth annotation. This article builds on our previous work by presenting a novel Functional Data Analysis based approach to assess the quality of annotations. Specifically, the bivariate annotation time-series are transformed into functions, such that each resulting functional annotation then becomes a sample element for analysis like Multivariate Functional Principal Component Analysis (MFPCA) that evaluate variation across all annotations. The resulting scores from MFPCA provide interesting insights into annotation patterns and facilitate the use of multivariate statistical techniques to address both (i) and (ii). Given the presented efficacy of these methods, we believe they offer an exciting new approach to assessing the quality of annotations.