Hi Csaba!
Just an idea: maybe you are using the "simple" interface, and this creates or tries to create new CP pairs before new alignment of (new) images? I am not sure, because I don't use this interface; I think it is intended for beginners and aiming to create a panorama "at once" from a given set of photos. And of course in your case you are feeding and growing an initial set of photos (your # 3) , and starting a recipe meant to be run just once when you press align (#1) and this starts with "create CPs".
I advise you to try at least the advanced interface. In this case you will "align" only when you optimize the panorama parameters, and this process does not create new CPs. You will have to create the CPs beforehand, and you can improve or create yourself new CPs when desidered -- and they will take effect after a subsequent optimization. A rule of thumb is optimization of 'positions only', and when the result seemed OK (or almost), then you could include 'positions and visualization', etc. For a correct 'visualization' optimization the panorama must be a complete turn around, and this is the case with your cylindricals.
As for the stacks, I think some photos could have an excessive superposition and/or the same kind of image content and this could fool Hugin.
Try please the advanced interface and tell us your progress. Goof luck!
regards,
Luis Henrique