That does sound like a puzzle.
I'm not sure what you have with the web based trial of V12 - I assume it's not something that is currently downloadable.
Further more i cannot immediately recall when the last major change to the PDF interpretation engine was implemented although my recollection was that it might have been in place since at least the start of V12.
To the best of my knowledge for every update of the PDF engine over the years there has always been a backwards compatibility mode available. All of the "old" specification engines have been included in later, enhanced, versions to avoid the need to re-work models where no changes were required.
Obviously that does not necessarily apply to what you are trying to do but it you have already checked that the same engine version is being used AND you are using exactly the same pdf file with both program versions it certainly sounds strange.
Do you have a sample of the report that you could share privately?
If so I could take a look at it and give you a second opinion. I have random distribution of 11, 12 and the latest 13 available - plus some much older stuff if I fire up some ancient machines. So I have some potential for comparing how the file is handled over time which should allow me to spot and report differences as they evolve.
That said there can be a huge challenge with PDF files and their internal structure depending on how and when they were created and which PDF writer creation engine was used. The engines are by no means equal to each other and do not always produce results that are consistent enough to make use of the same Monarch/(Modeler) model without adaptation.or some special model creation technique approaches that try to address the variability.
I appreciate that statement will sound vague or worse but it really can be impossibly to make any useful and pertinent observations without seeing a problem PDF file and the way a number of conversion to text programs handle it - including those programs from Adobe that offer such capability.
I hope this helps in some way.