There are several ways to get vim autoindent your code (set autoindent, set smartindent, set cindent, etc). When I first tried to use autoindenting I also faced your problem with comment outdenting, and later on I found a method to get rid of this "feature". So try this (put this to your .vimrc and comment out any other type of autoindenting)

filetype indent on
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Probably this also helps you to get your desired indent level:

autocmd FileType perl set softtabstop=3
autocmd FileType perl set shiftwidth=3
autocmd FileType perl set tabstop=3
autocmd FileType perl set expandtab
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