I think you need to show more of the code. Here is what I get with your three examples:
$ echo "foo
> bar
> baz
> " | perl -e 'my @a = <STDIN>; print @a'
foo
bar
baz
$ echo "foo
> bar
> baz
> " | perl -e 'my @a = <STDIN>; print "\n @a"'
foo
bar
baz
$ echo "foo
> bar
> baz
> " | perl -e 'my @a = <STDIN>; chomp(@a); print @a'
foobarbaz$
Do you do other manipulations of STDIN?
Update: Hmmmm, that is strange. I think chromatic's suggestion of something funny in the input file is likely. Also, do you (maybe in some init file) set $[=1; to get one-based indexing? That doesn't seem likely, but this is a puzzler.
After Compline,
Zaxo
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