Your example as given works fine here, maybe you should post the code you're actually using?

C.

Test:

perl -le'$ret_val = my_sub(1, "", 2, "", "", 3); sub my_sub{$arg1 = sh
+ift;$undef1 = shift;$arg2 = shift;$undef2 = shift;$undef3 = shift;$ar
+g3 = shift; print "Arg1:", $arg1, " Undef1:", $undef1, " Arg2:", $arg
+2, " Undef2:", $undef2; }'

Prints:
Arg1:1 Undef1: Arg2:2 Undef2:
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