I can't reproduce your issue on my Windows 7:

D:\progs\perl>YA_ARGV_test.pl foo bar baz
foo
bar
baz
foo
bar
baz

C:\>assoc .pl
.pl=Perl

C:\>ftype perl
perl="C:\Perl\bin\perl.exe" "%1" %*
[download]

Same perl, same Windows config (except that it's Windows 7 Professional).

Update: %PATHEXT% seems a red herring:

C:\>echo %pathext%
.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC;.py;.pyw;.RB;.RB
+W
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Note the absence of .PL.