POD has to start at the beginning of a line, try to anchor your = there.

Seems like your regex is backtracking from the end after anchoring at \n, Perl has heuristics to decide if it starts searching from the back or from the start.

And if it's not parsing line by line but the whole file, you might end up with an exponential growth by file size (try benchmarking other file sizes)

I have to say some of your regexes so far look broken and badly tested, it's not Perl's fault if it's not performing optimal.

And PLEASE try to provide a SSCCE including input data to facilitate us helping instead of speculating.