I'd say the short answer is "yes"

That's encouraging - thanks kcott

You've included completely unknown code with "use cPanelUserConfig;"

cPanelUserConfig is a cPanel module. It performs some magic with @INC so that user installed modules can be found by Perl. PDF::API2 is a module I have installed so without cPanelUserConfig we won't get very far. Pretty much every script I write server side has this so I can be pretty sure this is not the cause of the issue.

I'd move strict and warnings to the start of your code. Was there a reason for putting these in the middle of the script?

As both strict and warnings operate for all the block regardless of where they are declared, I tend to use them to separate the head code from the actual mechanics of code. I'm sure there are proper terms that I don't know but by "head code" I mean the part of the code that sets thing up correctly such as the shebang, setting paths and bringing in modules to use. Everything below is what actually does the work of the script.

Your report suggests that you think PDF::API2 is the source of the problem, but you don't say why

Sorry - I should have explained that identical head code exists in all the other scripts on the site and they all run with taint mode on. It's only since I tried using PDF::API2 that I have had this problem and the error reports it as being in File which is used by PDF::API2 and not called by my script anywhere else.

I'm out of the office currently but will look at the other things you suggest a little later and try removing/substituting code until I find the exact cause of the issue.