help needed with fraction of unexplained variance

Hello,

I have a data set that has 100000 observations and 200 variables. I have used PCA and luckily only 5 dimensions capture ~95% of the variance. I got this quantity from the eigenvalues of the covariance matrix.

Just to check that everything makes sense I have also calculated the fraction of unexplained variance as defined here: http://en.wikipedia.org/wiki/Fraction_of_variance_unexplained

To my surprise I got results that are inconsistent with the what I obtained from the eigenvalues of the covariance matrix. My question is how the two quantity relates to each other? I want to test some other dimension reducing techniques on the data as well and would be interested in making an apple-to-apple comparison among them in terms of the percentage of the original data retained.

Any help would be very much appreciated!

Best regards, Blaise