I suspect that anyone who does an upgrade will have this problem too.
Using Tiki the way you use it and enabling the features you enabled. 🤷🏻♂️
I don't use ElFinder and have no issues with PDF and uploading JPG files.
I use the last 26 Git version with all the fixes and improvement that should be released soon in Tiki26.1.
Did you try to reproduce your issue with the daily built ?
I recall an issue with the max width and height creating a broken archive.
May be on your Tiki check it is not set ? (or create a new file gallery without any parameter changes)