I beleive the issue you have, or may have resolved by now, is caused by the findpeaks input arguments. findpeaks has changed since MATLAB2014a. Currently findpeaks accepts a vector of indicies as the second argument for which [~,locs] is identified by. The 2014a version does not handle this index array as the second function argument. 2014a is looking for a string such as 'Tolerance' for the second input. 2014a findpeaks will output locs which may not precisely be the locs you want if you search only a portion of your signal for peaks.
To work around this and output the peak locs identified by 2014a I modified my code below:
% Find Peak Change in Covariance - Evaluated 99% Probability
% 2014b or later Version
[~,peakIx]=findpeaks(qCovAvg(100:end),Ix(100:end),'MinPeakHeight',q99);
% 2014a or Earlier Version
[~,peakIx] = findpeaks(qCovAvg(100:end),'MinPeakHeight',q99);
dumIx = Ix(100:end);
peakIx = dumIx(peakIx);
% Hope you find this helpful
