Looks like the model is too overfitted on post training to obey any system instructions. Just be thankful it is not like o3, producing dumb tables and em-spaces as code indentation and filling code with multi-byte code points.
You have a short window to enjoy gpt-4.5
to follow instructions before they flip the off switch on the only AI that is powered by IQ.
You could probably write up a regex for this. Even just replacing \n\n with \n if you want it to hit the entire document.