This is the default cp behaviour. You can see the same behaviour from the commandline:

[wine@guppie tmp_]$ touch boe
[wine@guppie tmp_]$ chmod u+x boe
[wine@guppie tmp_]$ su
Password: 
guppie:/home/wine/tmp_# cp boe boe.2
guppie:/home/wine/tmp_# ls -l
total 0
-rwxr--r--    1 wine     wine            0 Jul 23 12:35 boe
-rw-r--r--    1 root     wine            0 Jul 23 12:36 boe.2
guppie:/home/wine/tmp_#
[download]

This happens when a user (or perl in this case) copies files that do not belong to himself. The copies get chown-ed to the user.

I guess the only way to circumvent this is to restore the properties manually, if you have the permission to do that, that is.