As always: We cannot help without a sample of the data where problems can be reproduced, analyzed and described. Sorry, we don't have crystal balls. So if you want to help us solve an issue related to specific data, or possibly a bug (damn, I am not perfect, sorry), then we need the specific data. Or a crystal ball, at your option.
Let's try the first option first. Can you upload a complete and sufficient data set where this problem can be reproduced consistently (dropbox, etc)? Thank you so much in advance.