The substitution problem was first reported by an editor who indeed posted the message before confirming the decision. However, after that I have made several experiments, and I can safely state that this is not a decisive factor.
Even in case of recorded decision, this problem does occur.
It has to be mentioned, that there are email templates in the system that work perfectly all right. I have no problems with typical tasks such as sending articles for review or acknowledgement of article submission.
As for an upgrade. I have indeed made an update fairly recently. It was a significant one, as I have jumped from 2.2.4 to 2.3.6 skipping few editions along the way. The update created few problems, but apart from the need of relocating some icons etc., everything went smoothly. It wasn't until one of editors complained that I have realised that there is a problem email templates. The "Editorial Decison" e-mail templates are not too frequently usedin our journals, that is why it took me a while to realise that there is a problem with them.
As for the repetitions on the list of tempaltes. I have examined those repeated entries and the look completely identical to me. However, I cannot remove them directly, as there is no "Remove" option for default templates.