For multivariate data, when testing homogeneity of covariance matrices arising from two or more groups, Bartlett's (1937) modified likelihood ratio test statistic is appropriate to use under the null hypothesis of equal covariance matrices where the null distribution of the test statistic is based on the restrictive assumption of normality. Zhang and Boos (1992) provide a pooled bootstrap approach when the data cannot be assumed to be normally distributed. We give three alternative bootstrap techniques to testing homogeneity of covariance matrices when it is both inappropriate to pool the data into one single population as in the pooled bootstrap procedure and when the data are not normally distributed. We further show that our alternative bootstrap methodology can be extended to testing Flury's (1988) hierarchy of covariance structure models. Where deviations from normality exist, we show, by simulation, that the normal theory log-likelihood ratio test statistic is less viable compared with our bootstrap methodology. For functional data, Ramsay and Silverman (2005) and Lee et al (2002) together provide four computational techniques for functional principal component analysis (PCA) followed by covariance structure estimation. When the smoothing method for smoothing individual profiles is based on using least squares cubic B-splines or regression splines, we find that the ensuing covariance matrix estimate suffers from loss of dimensionality. We show that ridge regression can be used to resolve this problem, but only for the discretisation and numerical quadrature approaches to estimation, and that choice of a suitable ridge parameter is not arbitrary. We further show the unsuitability of regression splines when deciding on the optimal degree of smoothing to apply to individual profiles. To gain insight into smoothing parameter choice for functional data, we compare kernel and spline approaches to smoothing individual profiles in a nonparametric regression context. Our simulation results justify a kernel approach using a new criterion based on predicted squared error. We also show by simulation that, when taking account of correlation, a kernel approach using a generalized cross validatory type criterion performs well. These data-based methods for selecting the smoothing parameter are illustrated prior to a functional PCA on a real data set.