Your code looks okay, there is no glaring cause of why it would not loop correctly over all of your data files. Have you checked the data files themselves? Have they been correctly named?
Print the contents of filenames: does it have all different filenames? Try this:
numel(unique(filenames))
and check that the answer is 25. Then inside your loop add
disp(thisfile)
Perhaps the cause is the indexing around the ecgs variable, where there is possibly some confusion about row/column indexing:
ecgs = matstruct.val(1,:); % all columns ?
for rownum = 1:size(ecgs,1) % now all rows ?
ecg = ecgs(rownum,:); % each row... ?
results{K,rownum}= ... % placed in each column...
Perhaps you need to check that indexing.
