I'm afraid I don't understand what you gain by having 2.4 million lines of data attached as part of the perl script. Have you really not tried putting those first 13 lines into a separate file, so that the 2.4 million lines of data can sit alone (without the script attached) in a separate file, which your separate perl script then reads "in the normal way"?

Apart from that, it wouldn't surprise me to learn that a "modern" windows OS is still having (or making) trouble when more than one process wants to open the same file, and one of those processes wants write access on the file.

(Have you tried putting print "starting now\n"; as the 3rd line, to see if you get any output at all before the error message?)